Integrated sample-processing system

ABSTRACT

The invention provides an integrated sample-processing system and components thereof for preparing and/or analyzing samples. The components may include a transport module, a fluidics module, and an analysis module, among others.

FIELD OF THE INVENTION

[0001] The invention relates to sample-processing systems, and moreparticularly to integrated sample-processing systems and componentsthereof for preparing and/or analyzing samples.

BACKGROUND

[0002] Modern laboratory techniques such as high-throughput screening ofcandidate drug compounds may involve preparing and analyzing hundreds ofthousands or millions of samples. Recently, the processing of suchsamples has been facilitated by packaging samples in high-density sampleholders, such as microplates, for analysis together in an automateddevice. FIG. 1 shows an offset stack of microplates, illustrating therange in possible well densities and well dimensions. Plate 130 has 96sample wells. Plate 132 has 384 wells. Plate 134 has 1536 wells. Plate136 has 3456 wells. Plate 138 has 9600 wells.

[0003] Unfortunately, prior systems for processing large numbers ofsamples have significant shortcomings. For example, prior systems maynot have the flexibility to process sample holders with different sampledensities, or the sensitivity or accuracy to process sample holders withvery small samples. Moreover, prior systems may be limited to single(unit) operations, meaning, for example, that they can dispense samplesor analyze samples, but not do both. Thus, prior systems may requiredifferent apparatus for different applications, or lead to missed hits,limited research capabilities, lower throughput, and/or increased costsfor compounds, assays, and reagents.

SUMMARY OF THE INVENTION

[0004] The invention provides an integrated sample-processing system andcomponents thereof for preparing and/or analyzing samples. Thecomponents may include a transport module, a fluidics module, and ananalysis module, among others.

BRIEF DESCRIPTION OF THE DRAWINGS

[0005]FIG. 1 is a top view of overlapping microplates showing variationsin well size and well density.

[0006]FIG. 2 is a perspective view of a system for preparing and/oranalyzing samples.

[0007]FIG. 3 is a perspective view of an alternative system forpreparing and/or analyzing samples.

[0008]FIG. 4 is a schematic view of a generalized system for preparingand/or analyzing samples.

[0009]FIG. 5 is a top view of a 96-well microplate constructed inaccordance with aspects of the invention.

[0010]FIG. 6 is a cross-sectional view of the microplate in FIG. 5,taken generally along line 6-6 in FIG. 5.

[0011]FIG. 7 is a first enlarged portion of the cross-sectional view inFIG. 6, showing details of a sample well.

[0012]FIG. 8 is a second enlarged portion of the cross-sectional view inFIG. 6, showing details of a reference fiducial.

[0013]FIG. 9 is a top view of a 384-well microplate constructed inaccordance with the invention.

[0014]FIG. 10 is a cross-sectional view of the microplate in FIG. 8,taken generally along line 10-10 in FIG. 9.

[0015]FIG. 11 is an enlarged portion of the cross-sectional view in FIG.10, showing details of a sample well.

[0016]FIG. 12 is an enlarged cross-sectional view of the microplate inFIG. 9, taken generally along line 12-12 in FIG. 9, showing details of areference fiducial.

[0017]FIG. 13 is a perspective view of a 1536-well microplateconstructed in accordance with the invention.

[0018]FIG. 14 is a top view of the microplate in FIG. 13.

[0019]FIG. 15 is an enlarged portion of the top view in FIG. 14, showingdetails of the sample wells.

[0020]FIG. 16 is a cross-sectional view of the microplate in FIG. 14,taken generally along line 16-16 in FIG. 14.

[0021]FIG. 17 is an enlarged portion of the cross-sectional view in FIG.16, showing details of the sample wells.

[0022]FIG. 18 is a partial perspective view of a transport moduleconstructed in accordance with aspects of the invention.

[0023]FIG. 19 is a partially exploded perspective view of a latchmechanism from the transport module of FIG. 18.

[0024]FIG. 20 is a cross-sectional view of the latch mechanism of FIG.19, taken generally along line 20-20 in FIG. 19, showing the latchmechanism in use supporting a stack of plates.

[0025]FIG. 21 is a multi-panel time-lapse cross-sectional view of thelatch mechanism of FIG. 20, showing the latch mechanism in use to inputa plate from a stack of plates.

[0026]FIG. 22 is a multi-panel time-lapse cross-sectional view of thelatch mechanism of FIG. 20, showing the latch mechanism in use to outputa plate to a stack of plates.

[0027]FIG. 23 is a partially exploded perspective view of an intrasitedriver from the transport module of FIG. 18.

[0028]FIG. 24 is a partially exploded perspective view of an intersitedriver from the transport module of FIG. 18.

[0029]FIG. 25 is a partially schematic view of a noncontact fluiddispenser, showing a positive-displacement syringe pump withsapphire-tipped dispense elements.

[0030]FIG. 26 is a partially schematic view of an alternative noncontactfluid dispenser, showing a positive-displacement syringe pump withsolenoid valves and sapphire-tipped dispense elements.

[0031]FIG. 27 is a partially schematic view of another alternativenoncontact fluid dispenser, showing a positive-pressure pump withsolenoid valves and sapphire-tipped dispense elements.

[0032]FIG. 28 is a schematic view of yet another alternative noncontactfluid dispenser, showing the relationship between fluid reservoirs,pumps, and dispense elements for the fluid dispenser shown (togetherwith a transport module and an analysis module) in FIG. 2 as part of anintegrated system for preparing and/or analyzing samples.

[0033]FIG. 29 is a perspective view of a dispense driver for the fluiddispenser of FIG. 28, showing the relationship between the dispenseelements and a sample holder. The view is an enlargement of componentsshown in FIG. 18 in connection with a transport module.

[0034]FIG. 30 is a front view of a portion of the fluid dispenser ofFIG. 28, showing a fluid control unit including a bank of associatedsyringe pumps.

[0035]FIG. 31 is a front view of a bank of dispense elements for thefluid dispenser of FIG. 28.

[0036]FIG. 32 is an exploded perspective view of the bank of dispenseelements shown in FIG. 31.

[0037]FIG. 33 is a cross-sectional view of a portion of the bank ofdispense elements shown in FIG. 32, taken generally along line 33-33 inFIG. 32.

[0038]FIG. 34 is a six-panel, time-lapse schematic view of a single pinfrom a pin transfer device, showing how the device may be used totransfer fluid.

[0039]FIG. 35 is a schematic view of a pin transfer device andassociated sample holder, showing shortcomings associated with a rigidarray of pins.

[0040]FIG. 36 is a perspective view of an alternative pin transferdevice and associated sample holder.

[0041]FIG. 37 is a cross-sectional view of the alternative pin transferdevice and associated sample holder of FIG. 36, taken generally alongline 37-37 in FIG. 36.

[0042]FIG. 38 is a partially schematic top view of avariable-pitch-array fluid dispenser, showing the dispenser in use witha microplate.

[0043]FIG. 39 is a partially schematic side view of thevariable-pitch-array fluid dispenser and microplate of FIG. 38, takengenerally along line 39-39 in FIG. 38.

[0044]FIG. 40 is a perspective view of a microplate sealing systemconstructed in accordance with aspects of the invention.

[0045]FIG. 41 is a perspective view of a sealed microplate.

[0046]FIG. 42 is a top view of a microplate sealing system, shownapplying sheets to a microplate.

[0047]FIG. 43 is a top view of a microplate sealing system, shownremoving sheets from a microplate.

[0048]FIG. 44 is a schematic view of a system for controlling ambientconditions around samples contained in wells in a stack of microplatesin accordance with aspects of the invention.

[0049]FIG. 45 is a side view of a microplate having an aperture in thebase to allow thermal and gas circulation below sample wells containedin the microplate and projections for supporting another microplate.

[0050]FIG. 46 is a perspective view of portions of two alternativeembodiments of a lid-spacer for separating stacked microplates.

[0051]FIG. 47 is a side view of alternated stacked microplates andlid-spacers being manipulated by singulation latches.

[0052]FIG. 48 is a schematic view of a sample processing systemutilizing lid-spacing devices in an incubating station.

[0053]FIG. 49 is a partially exploded perspective view of a system foranalyzing samples in accordance with aspects of the invention, showing atransport module and an analysis module.

[0054]FIG. 50 is a schematic view of an optical system from the analysismodule of FIG. 49.

[0055]FIG. 51 is a partially schematic perspective view of the apparatusof FIG. 50.

[0056]FIG. 52 is a schematic view of photoluminescence opticalcomponents from the apparatus of FIG. 50.

[0057]FIG. 53 is a schematic view of chemiluminescence opticalcomponents from the apparatus of FIG. 50.

[0058]FIG. 54 is a top perspective view of a portion of a transportmechanism from the analysis module of FIG. 49.

[0059]FIG. 55 is a bottom perspective view of the portion of a transportmechanism shown in FIG. 54.

[0060]FIG. 56 is a partial cross-sectional view of the portion of atransport mechanism shown in FIGS. 54 and 55, taken generally along theline 56-56 in FIG. 55.

[0061]FIG. 57 is a perspective view of a base platform and associateddrive mechanisms for moving the portion of a transport mechanism shownin FIGS. 54-56 along X and Y axes relative to the base platform.

DETAILED DESCRIPTION OF THE INVENTION

[0062]FIG. 2 is a perspective view of a system 500 for preparing and/oranalyzing samples. System 500 includes at least one input/output (I/O)site 502 for sample input and output, and a plurality of functionmodules (or stations) for performing a plurality of functions, includinga transport module 504, a fluidics module 506, and an analysis module508. The transport module participates in sample transport, for example,by shuttling a sample or sample holder between the I/O sites, fluidicsmodule, and analysis module. The fluidics module participates in samplepreparation, for example, by adding (and/or removing) a component of asample to a sample holder. The analysis module participates in sampleanalysis, for example, by performing an optical analysis of a samplebased on photoluminescence, chemiluminescence, absorbance, andscattering, among others. The components of system 500 may be configuredto enhance function, convenience, and/or appearance.

[0063]FIG. 3 is a perspective view of an alternative system 600 forpreparing and/or analyzing samples. System 600 resembles system 500 andsimilarly includes at least one I/O site 602, a transport module 604, afluidics module 606, and an analysis module 608. However, in system 600,the I/O sites include processing bins 610 to facilitate handlingmultiple sample holders. Moreover, the fluidics module and the transportand analysis modules are positioned on different shelves of a moveablemulti-tiered cart 612, enhancing portability and reducing footprint (<1square meter).

[0064]FIG. 4 is a schematic view of a generalized system 700 forpreparing and/or analyzing samples. System 700 includes at least one I/Osite 702 and a plurality of function modules, including a transportmodule 704, a fluidics module 706, and an analysis module 708, as above,as well as N auxiliary modules 710 associated with redundant and/oradditional functionalities, such as cleaning, sealing, storage, samplepreparation, etc. Here, N may range from zero to several or more. Acleaning module might include components for emptying and/or cleaningsample holders. A sealing module might include components for sealing,unsealing, and/or otherwise covering and uncovering sample holders. Anincubation module might include components for incubating sample holdersand their associated samples, with environmental control of atmosphere,temperature, agitation, and so on. A sample preparation module mightinclude components for particular sample-preparation functions, such asa thermocycler for performing heating and cooling during the polymerasechain reaction (PCR).

[0065] Function modules generally include one or more function sites atwhich a corresponding function is performed. For example, a fluidicsmodule may include a dispense site 712 at which a fluid is dispensed, ananalysis module may include an examination (“exam”) site 714 at which asample is analyzed, and an auxiliary module may include an auxiliarysite 716 at which an auxiliary function is performed, such as cleaning,sealing, storage, etc. A transport module may be connected directly orindirectly with I/O sites 702 for sample input and output, and with oneor more of the function sites. If the transport module is connectedindirectly to a function (or I/O) site, the transport module might handoff a sample holder at a transfer site to a separate transport mechanismassociated with the respective function module. A transport module alsomay be connected to additional robotics for providing and removingsample holders from the I/O sites.

[0066] System 700 generally may include any desired combination offunction modules. For example, a simple system may include a pair ofmodules, such as a fluidics module and a transport module, or ananalysis module and a transport module. These systems might be used toprepare a sample or analyze a sample, respectively. A more complexsystem may include several modules, such as a fluidics module, ananalysis module, an incubation module, and a transport module. This morecomplex system might be used to prepare a sample, analyze a sample, orboth prepare and analyze a sample, for example, by adding a reporter tothe sample using the fluidics module, incubating the sample using theincubation module, reading the sample using the analysis module, andinputting, outputting, and transporting the sample using the transportmodule.

[0067] The function modules generally may be accessed in any desiredorder. For example, a sample might be analyzed only after fluiddispensing, or both before and after fluid dispensing if a multi-stepassay is being performed and/or if a background is being subtracted. Theorder of access may be controlled using a controller that may scheduleand initiate singulation of samples to and from I/O sites, transportbetween sites, dispensing at a dispensing site, and/or analysis at ananalysis site. The order and timing of such movements will depend on thenature of the assay and generally will differ for kinetics assays (wheretiming is crucial) and endpoint assays (where timing is not crucial, solong as an endpoint has been reached).

[0068] The function modules generally may be combined or integrated inany desired way. For example, a single module may perform fluidics andcleaning operations, and a single transport mechanism may access any orall of the I/O and/or function sites.

[0069] Further aspects of the invention are presented in the followingsections: (A) sample holders, (B) transport module, (C) fluidics module,(D) auxiliary modules, (E) analysis module; and (F) additional examples.

A. Sample Holders

[0070] The system and its components may be used with a variety ofsample holders and sample holder features. As used here, “sample holder”generally comprises any substrate or material capable of supporting asample so that the sample holder and associated sample can betransported by an automatic transport module and subjected to a functionsuch as fluid dispensing or optical analysis at a corresponding functionmodule. Sample holders may be used alone, in stacks, or in combinationwith seals or covers, as described below. Sample holders may supportsamples at low, intermediate, or high density, and be designed forsingle or multiple use.

[0071] Exemplary sample holders include microplates, PCR plates,biochips, and chromatography plates, among others. A microplate is amulti-well sample holder, typically but not exclusively used forluminescence applications. Preferred microplates are described below. APCR plate is a multi-well sample holder used for performing PCR.Preferred PCR plates would include a footprint, well spacing, and wellshape similar to those of the preferred microplates, while possessing astiffness adequate for automated handling and a thermal stabilityadequate for PCR. A biochip is a small, flat surface (such as a glass orsilicon wafer) onto which biomolecules (such as nucleic acids andproteins) are immobilized in distinct spots or arrays. Biochips includeDNA chips, DNA microarrays, gene arrays, and gene chips, among others.Preferred biochips are described in Bob Sinclair, Everything's GreatWhen It Sits on a Chip: A Bright Future for DNA Arrays, 13 THESCIENTIST, May 24, 1999, at 18. A chromatography plate is a flat surfaceused for performing chromatography, such as thin-layer chromatography.

[0072] Microplates are a preferred sample holder, and the system and itscomponents may be designed for use with microplates having some or allof the following features. For example, suitable microplates may includemicroplates having any number of wells, including 96, 384, and 1536,among others. Suitable microplates also may include microplates havingwells with elevated bottoms, frusto-conical shapes, and/or low volumes,or wells configured to reduce the formation and/or trapping of bubbles,as described in the following U.S. patent applications, which areincorporated herein by reference: Ser. No. 08/840,553, filed Apr. 14,1997; and Ser. No. 09/478,819, filed Jan. 5, 2000. Suitable microplatesalso may include microplates having reference fiducials in or around aperimeter portion of the microplate (or elsewhere), as described in PCTPatent Application Ser. No. PCT/US99/08410, filed Apr. 16, 1999, whichis incorporated herein by reference. Such reference fiducials may bemolded into the plate and/or applied to the plate by silkscreen, colortransfer, hot stamping, and/or application of reflective paint, amongothers. Suitable microplates also may include microplates having abarcode for reading by a barcode reader, as described in U.S. patentapplication Ser. No. 09/160,533, filed Sep. 24, 1998, which isincorporated herein by reference. Suitable microplates also may beuseable in combination with seals for sealing individual wells in amicroplate, and/or spacer members for separating individual microplatesin a stack, as described below.

[0073] FIGS. 5-17 show a set of preferred microplates that have similarheights and footprints but that differ in well shape, well size, and/orwell density. These microplates include (1) 96-well microplates, (2)384-well microplates, (3) 1536-well microplates, and (4) miscellaneousmicroplates.

[0074] 1. 96-Well Microplates

[0075]FIG. 5 is a top view of a 96-well microplate 1200 constructed inaccordance with aspects of the invention. Microplate 1200 includes aframe 1202 and a plurality of sample wells 1204 disposed in the frame.In some embodiments, microplate 1200 may include one or more referencefiducials 1206 disposed in the frame.

[0076] Frame 1202 is the main structural component of microplate 1200.The frame may have various shapes and various dimensions. In microplate1200, frame 1202 is substantially rectangular, with a major dimension Xof about 127.8 mm and a minor dimension Y of about 85.5 mm. Tolerancesin plate dimensions typically are about ±0.5-1.0 mm for polystyreneplates, but may increase to about ±2 mm for polypropylene plates,especially if the polypropylene plates are produced using molds designedfor polystyrene plates. Frame 1202 may be adapted for ease of use andmanufacture. For example, frame 1202 may include a base 1208 tofacilitate handling and/or stacking, and frame 1202 may include notches1210 to facilitate receiving a protective lid. Frame 1202 may beconstructed of a material, such as a thermoplastic, that is sturdyenough for repeated, rugged use and yet minimally photoluminescent toreduce background upon illumination.

[0077] Frame 1202 includes a sample well region 1212 and an edge region1214 forming a perimeter 1216 around the sample well region. Samplewells may be disposed in the sample well region in variousconfigurations. In microplate 1200, sample wells 1204 are disposed insample well region 1212 in a substantially rectangular 8×12 array, witha pitch (i.e., center-to-center interwell spacing) along both X and Y ofabout 9 mm. This pitch corresponds to a density of wells of about onewell per 81 mm ².

[0078] Reference fiducials 1206 may be used for identification,alignment, and/or calibration of the microplate. Reference fiducials maybe disposed in the sample well region and/or the edge region in variousconfigurations. In microplate 1200, reference fiducials 1206 aredisposed in edge region 1214, substantially aligned with a row of samplewells along the X dimension, although reference fiducials also may beoffset from the rows of sample wells. Reference fiducials preferentiallyare positioned in comers of the microplate, near where optical analysisbegins, so that they may quickly be identified and analyzed. Referencefiducials may be positioned in rotationally symmetric positions, so thatmicroplates may be loaded into an optical device and analyzed backwardswithout difficulty. Alternatively, reference fiducials may be positionedin rotationally asymmetric positions, so that the system can ascertainwhich way the microplate is oriented; information on orientation isuseful because samples typically are not positioned symmetrically withinthe microplate. Further aspects of reference fiducials are described inPCT Patent Application Ser. No. PCT/US99/08410, filed Apr. 16, 1999,which is incorporated herein by reference.

[0079]FIG. 6 is a cross-sectional view of microplate 1200, showingsample wells 1204, reference fiducial 1206, and base 1208. In microplate1200, frame 1202 has a top 1218, a substantially parallel bottom 1220,and substantially perpendicular sides 1222. Top 1218 may have variousshapes, although it typically is flat. (Top 1218 may be surrounded by araised edge to facilitate stacking.) Frame 1202 has a height H of about12 mm, corresponding generally to the separation between top 1218 andbottom 1220. Tolerances in plate height typically are about 0.5 mm orless. Sample wells 1204 are disposed with open, optically transparentends 1224 directed toward top 1218, and closed, optically opaque ends1226 directed toward bottom 1220. In some embodiments, optically opaqueends 1226 may be replaced by optically transparent ends to permit bottomillumination and/or detection. Reference fiducial 1206 is disposed ontop 1218, although reference fiducials also may be disposed on bottom1220 and/or sides 1222.

[0080] The preferred plate height is determined by a variety ofconsiderations. Generally, taller plates with elevated bottoms and/orfilled wells put the samples closer to the detector for analysis,increasing numerical aperture and hence signal. Conversely, shorterplates allow more plates to be stacked into processing bins for longerperiods of unattended operation. The specified height of about 12 mmgenerally is large enough to facilitate handling by sample handlersand/or a stage, and yet small enough to permit optical analysis of theentire well. Moreover, the specified height generally is sufficient toensure that the microplates are sufficiently flat for analysis.

[0081]FIG. 7 is a first enlarged portion of the cross-sectional view inFIG. 6, showing details of sample wells 1204. Sample wells may havevarious shapes and various dimensions, as described in detail insubsequent sections. In microplate 1200, sample wells 1204 aresubstantially frusto-conical, with substantially straight side walls1228 and a substantially flat bottom wall 1230. In microplate 1200,optically opaque ends 1226 are positioned about 6.7 mm below top 1218,and about 5.3 mm above bottom 1220. Sample well 1204 is characterized bya top diameter D_(T,96), a bottom diameter D_(B,96), a height H₉₆, and acone angle θ₉₆. Here, θ₉₆ is the included angle between side walls 1228.In microplate 1200, D_(T,96) is about 4.5 mm, D_(B,96) is about 1.5 mm,H₉₆ is about 6.7 mm, and θ₉₆ is about 25.4°. Sample well 1204 has atotal volume of about 50 μL, and a smallest practical working volume ofabout 1-40 μL.

[0082]FIG. 8 is a second enlarged portion of the cross-sectional view inFIG. 6, showing details of reference fiducial 1206. Reference fiducialsmay have various shapes and various dimensions, as described in detailin subsequent sections. In microplate 1200, reference fiducial 1206 issubstantially frusto-conical, with substantially straight side walls1232 and a substantially flat bottom wall 1234. Reference fiducial 1206is characterized by a top diameter D_(T,RF,96), a bottom diameterD_(B,RF,96), a height H_(RF,96), and a cone angle θ_(RF,96). Here,D_(B,RF,96) and θ_(RF,96) are substantially equal to D_(B,96) and θ₉₆,the corresponding values for sample well 1204. H₉₆ is about 1 mm, andD_(T,RF,96) is specified by the other parameters. In some applications,the reference fiducial may contain a luminescent material or solution sothat it is easier to locate. In other applications, the referencefiducial may be used as a blank for determining background, or as anadditional sample well for holding an additional sample. In theseapplications, the reference fiducial may be located and/or analyzedusing the same optical system used to analyze samples in conventionalsample wells.

[0083] 2. 384-Well Microplates

[0084] FIGS. 9-12 are views of a 384-well microplate 1300 constructed inaccordance with aspects of the invention. Microplate 1300 is similar inmany respects to microplate 1200 and includes a frame 1302 and aplurality of sample wells 1304 disposed in a sample well region 1312 ofthe frame. In some embodiments, microplate 1300 may include one or morereference fiducials 1306 disposed in an edge region 1314 or other regionof the frame.

[0085] The external dimensions of microplate 1300 are similar to theexternal dimensions of microplate 1200. However, the density of samplewells in microplate 1300 is four times higher than the density of samplewells in microplate 1200. Consequently, the pitch (i.e., thecenter-to-center interwell spacing) in microplate 1300 is about 4.5 mm,or about one-half the pitch in microplate 1200. This pitch correspondsto a density of wells of about four wells per 81 mm². In microplate1300, reference fiducial 1306 is positioned about midway between tworows of sample wells along the X direction; in contrast, in microplate1200, reference fiducial 1206 is positioned about in line with a row ofsample wells along the X direction. This is because the referencefiducials are positioned in approximately the same position in eachmicroplate, but the center line of one row of sample wells in microplate1200 because the center line between two rows of sample wells inmicroplate 1300 as the density of wells is quadrupled.

[0086] Sample wells 1304 in microplate 1300 are similar to sample wells1204 in microplate 1200. Sample wells 1304 may be characterized by a topdiameter D_(T,384), a bottom diameter D_(B,384), a height H₃₈₄, and acone angle θ₃₈₄. The preferred values of D_(B,384) and θ₃₈₄ formicroplate 1300 are substantially similar to the preferred values ofD_(B,96) and θ₉₆ for microplate 1200. However, the preferred value forD_(T,384), which is about 4.7 mm, is smaller than the preferred valuefor D_(T,384), which is about 6.7 mm. In microplate 1300, the upperdiameter must be smaller than the upper diameter of the sample wells inmicroplate 1200, because the sample wells are close packed, leaving nomore interwell spacing than necessary for moldability. In turn, thepreferred value for H₃₈₄ is about 4.7 mm, so that the wells are elevatedby about 7.3 mm. Sample well 1304 has a total volume of about 25 μL, anda smallest practical working volume of about 1-12 μL.

[0087] Reference fiducial 1306 in microplate 1300 may be essentiallyidentical to reference fiducial 1206 in microplate 1200.

[0088] 3. 1536-Well Microplates

[0089] FIGS. 13-17 are views of a 1536-well microplate 1350 constructedin accordance with aspects of the invention. Microplate 1350 is similarin many respects to microplates 1200 and 1300, and includes a frame 1352and a plurality of sample wells 1354 disposed in the frame. The pitch inmicroplate 1350 is about 2.25 mm, or about one-half the pitch inmicroplate 1300 and about one-fourth the pitch in microplate 1200. Thispitch corresponds to a density of wells of about sixteen wells per 81mm².

[0090] Sample wells 1354 may be exclusively frusto-conical, like samplewells 1204 in microplate 1200 and sample wells 1304 in microplate 1300.However, due to spatial constraints, the volume of such wells would haveto be small, about 1-2 μL. Smaller wells are easier to mold and keepwithin tolerances, but they provide less flexibility and place morestringent demands on fluid dispensing and analytical equipment.Alternatively, sample wells 1354 may have a frusto-conical lower portion1306 coupled to a cylindrical upper portion 1308. The volume of suchwells may be larger, for example, about 7-8 μL. Larger wells are moredifficult to mold, but they permit use of a wider range of samplevolumes and therefor a wider range of assay formats. Larger samplevolumes may be useful if the microplate is used in conjunction withstandard fluid dispensing equipment, because the standard equipment mayhave difficulty dispensing small volumes. Larger sample volumes also maybe useful if reagents are to be added to the well from stock solutions,such as 100×DMSO or DMF stock solutions, because they make it lessnecessary to dispense very tiny amounts of stock solution to obtainadequate dilution. Larger sample volumes also may be useful forcell-based assays, because cells may live longer in a larger volume ofmedium.

[0091] Reference fiducials in microplate 1350 may be essentiallyidentical to reference fiducials 1206 in microplate 1200 and referencefiducials 1306 in microplate 1300. However, reference fiducials inmicroplate 1350 may be more important than reference fiducials in plates1200 and 1300 because the well dimensions in microplate 1350 mayapproach the molding tolerances, making it more likely that wells willbe significantly displaced from their nominal positions.

[0092] 4. Miscellaneous Microplates

[0093] The system and its components also may be designed for use withsome or all of the following microplates:

[0094] (a) A microplate having a frame portion and a top portion, wherean array of wells is formed in the top portion. The wells are organizedin a density of at least about 4 wells per 81 mm². Each well has abottom wall that is elevated at least about 7 millimeters above a planedefined by a bottom edge of the frame.

[0095] (b) A microplate having an array of conical wells organized in adensity of at least about 4 wells per 81 mm².

[0096] (c) A microplate having an array of conical wells, where eachwell has a maximum volume capacity of less than about 55 microliters. Apreferred small-volume well design has a volume capacity of 1-20microliters.

[0097] (d) A microplate having an array of wells in the top portion,where each well has a maximum volume capacity of less than about 55microliters and a well bottom that is elevated at least about 7millimeters above a plane defined by a bottom edge of the frame.

[0098] (e) A microplate having an array of wells in a top portion,organized in a density of at 2 least about 4 wells per 81 mm², whereeach well has a conical portion characterized by a cone angle of atleast about 8°.

[0099] (f) A microplate having an array of conical wells characterizedby a cone angle θ, where θ=2arcsin (NA/n) and NA is equal to or greaterthan about 0.07.

[0100] (g) A microplate having an array of wells organized in a densityof at least about 16 wells per 81 mm², where each well has afrusto-conical bottom portion and a substantially cylindrical upperportion.

[0101] (h) A microplate comprising a frame and a plurality offrusto-conical sample wells disposed in the frame, where the samplewells are characterized by a cone angle of at least about 8°. Themicroplate further may include a reference fiducial that providesinformation to facilitate sample analysis.

[0102] (i) A microplate having 864 sample wells, 3456 sample wells, or9600 sample wells.

[0103] (j) A microplate formed of black, white, or clear material, or acombination thereof.

[0104] (k) A microplate suitable for performing PCR.

B. Transport Module

[0105]FIG. 18 shows a transport module 2100 constructed in accordancewith aspects of the invention. The transport module generally comprisesany mechanism or system for automatically shuttling a plate or othersample holder between an I/O site and one or more function or transfersites. The transport module may enhance convenience by reducing humanintervention and enhance throughput by reducing the time required toprocess multiple samples.

[0106] The transport module may include one or more I/O sites 2102, oneor more function or transfer sites 2104, and mechanisms for movingplates between the I/O and function sites. An I/O site is a site atwhich sample holders are input and/or output. A function site is a siteat which one or more functions are performed, such as fluid dispensing,analysis, cleaning, containment, and/or incubation, among others. Atransfer site is a site at which a sample holder is transferred to atransport mechanism (independently) associated with a function module.The mechanisms for moving plates may include a latch mechanism 2106, anintrasite driver 2108, and/or an intersite driver 2110. The latchmechanism may be used for singulating plates from and to stacks ofplates. The intrasite and intersite drivers may be used for movingplates between and within sites, respectively. These latch mechanism anddrivers may share features and/or components, or be substantially ortotally independent.

[0107] The transport module also may include other features, such as abarcode reader 2120 for reading an informational barcode optionallyassociated with a plate, a plate sensor for detecting the presence of aplate at one or more sites within the transport module, and one or moreinterfaces for interactions with function modules. The plate sensors maybe positioned at one or more sites and may be configured to accommodatevariations in plate thickness, color, and so on. The interfaces mayinclude mounting sites for a dispense head 2124 and/or a dispense driver2126 associated with a fluidics function module.

[0108] The transport module may employ a variety of singulationstrategies, depending in part on the number of I/O sites, the nature ofthe I/O sites (i.e., input, output, or both), and the location in thestack from which plates are taken and/or added (typically bottom and/ortop). Transport module 2100 has two I/O sites, from which plates aretaken and/or added at the bottom. Typically, but not necessarily, one ofthese sites is dedicated to input, and the other is dedicated to output.To input a plate, a robot (1) removes a plate from the bottom of aninput stack of plates at the input site, (2) transports the plate to thetransfer site, and (3) transfers the plate at the transfer site to atransport mechanism for an associated function module. To output aplate, the robot (1) takes the plate from the transport mechanism forthe function module at the transfer site, (2) transports the plate tothe output site, and (3) transfers the plate at the output site to thebottom of an output stack of plates at the output site. In transportmodule 2100, these functions are performed by the intersite andintrasite drivers, with preferred throughputs ranging from about 1second per plate to about 5 seconds per plate.

[0109] Further aspects of the transport module are described in thefollowing sections: (1) latch mechanisms, (2) intrasite drivers, (3)intersite drivers, (4) additional features, and (5) examples.

[0110] 1. Latch Mechanisms

[0111] The latch mechanism generally comprises any mechanism forinputting a single plate from a stack of plates and/or outputting asingle plate to a stack of plates. The following description addresses(a) the actuation mechanism employed by the latch mechanism, and (b)general attributes of the latch mechanism.

[0112] a. Actuation Mechanism

[0113]FIG. 19 shows an exemplary latch mechanism 2200 for used in theI/O sites. Latch mechanism 2200 includes a latch body 2202 andcomplementary pairs of latches 2204, pivot pins 2206, retaining pins2208, torsion springs 2210, and electromagnets 2212. The latch body isan elongate substantially rectangular structure that includes aninward-facing recess 2214 adjacent each end. The latches are elongatestructures that include a pivot portion 2216 and a pick portion 2218.The latches are pivotably mounted in recesses 2214 so that the pivotportion is mounted about the pivot pin and the pick portion is free topivot through an angle determined by the retaining pin at one extremeand the electromagnet at the other extreme.

[0114] The latch mechanisms generally are used in pairs to supportopposite sides of a plate, and each latch mechanism includes two latchesto support opposite ends of a single side of the plate. As describedbelow, this combination of two lifters and four latches cooperates tosingulate single plates from and to the bottom of a stack of plates.

[0115]FIG. 20 shows latch mechanism 2200 in use to support a stack 2230of plates 2232 ^(a,b), which rest atop pick portions 2218 of latches2204 and generally above a lifter 2234. The pick portions are biasedinboard of latch body 2202 and into the cavity 2236 of the correspondingI/O site to support the plates by the torsion springs (not shown). Thelatch also may be biased toward this position by other mechanisms,including counterweights, electromagnets, and other types of springs.The latch also may be biased toward this position by having a center ofgravity above and inward of pivot pin 2206.

[0116]FIG. 21 shows a four-step input cycle for inputting (orsingulating) a plate using the transport module and associated latchmechanisms. Plates may be input from a stack before fluid dispensing andanalysis, and after incubation, among others.

[0117] Step 1. The first input step (Panel A) comprises raising lifters2234 to elevate a stack 2230 of plates 2232 a,b through contact of theplates with an upper surface 2240 of the lifters and to push latches2204 into a retracted position through contact of the latches with aside surface 2242 of the lifters. In the depicted embodiment, thelifters are raised from their resting height to their maximum height(about 5 mm), after which electromagnets 2212 behind each latch areenergized to hold the latch in the retracted position. In otherembodiments, the latches may be moved to and/or held in the retractedposition at alternative times and/or by alternative mechanisms, such asa solenoid-actuated pin. If it is unnecessary to reverse the function ofthe latch (for example, because the latch is used only for input), thelatch may be held in the retracted position by eliminating a notch 2244in the lifter that otherwise permits the pick portion of the latch tomove under the plates.

[0118] Step 2. The second input step (Panel B) comprises loweringlifters 2234 to lower stack of plates 2230. After pick portion 2218 oflatch 2204 has passed below a bottom edge 2250 of input plate 2232 a,the latches are released by de-energizing electromagnets 2212, so thatthe pick portion falls against and then rides along a side 2252 of theplate. The electromagnets thus control release of the latch withoutmoving parts. The input plate is the bottommost plate in the stack ofplates. Input-only latches, which lack a top notch, will ride along theside of the lifter and then fall against and ride along the side of theplate automatically.

[0119] Step 3. The third input step (Panel C) comprises further loweringlifters 2234, with pick portion 2218 of latch 2204 continuing to ridealong the side of input plate 2232 a. The pick portion will follow thecontour of the plate, eventually falling onto the narrower upper sectionof the plate, where the pick portion will be positioned below a bottomsurface 2260 of the second to the bottommost plate 2232 b in the stack.

[0120] Step 4. The fourth input step (Panel D) comprises furtherlowering lifters 2234 until input plate 2232 a moves below pick portion2218 of latch 2204 and the pick portion contacts bottom surface 2260 ofsecond to the bottommost plate 2232 b. The latch thereby catches thenext plate, preventing it from dropping, while the input plate remainson the lifter for further lowering. Thus, the lifter retains a singleplate, and the latch retains the rest of the original stack of plates.The angle of the top of the latch may be such that the normal force fromthe weight of the stack is directed through pivot pin 2206, so that noadditional moments are induced on the latch. At this point, a plate hasbeen singulated for further transport to a dispense site, an analysissite, or an auxiliary site, as desired.

[0121]FIG. 22 shows a four-step output cycle for outputting a plateusing the transport module and associated latch mechanism. Plates may beoutput after fluid dispensing and/or analysis, among others. The latchmechanism functions passively as an output latch but actively as aninput latch, in that the electromagnets are not energized during theoutput cycle but are energized for a brief portion of the input cycledown stroke.

[0122] Step 1. The first output step (Panel A) comprises positioning anoutput plate 2280 a (i.e., a plate to be output) on lifter 2234 andraising the lifter to elevate the plate so that it is positioned beneaththe bottommost plate 2280 b in a stack of plates 2282 to which it is tobe added or returned. As the lifters raise the plate, latches 2204 arepushed out of the way by the outer contour of the plate.

[0123] Step 2. The second output step (Panel B) comprises furtherraising lifter 2234 until a top surface 2290 of output plate 2280 acontacts a bottom surface 2292 of bottommost plate 2280 b in stack 2282.The new stack is then lifted above latch 2204.

[0124] Step 3. The third output step (Panel C) comprises lowering lifter2234 so that pick portion 2218 of latch 2204 can drop into notch 2244 inthe lifter, thereby positioning itself beneath the new stack of plates2282′.

[0125] Step 4. The fourth output step (Panel D) comprises furtherlowering lifter 2234 to its resting position, leaving output plate 2280a in stack 2282′.

[0126] Except as noted above, the output cycle generally resembles theinput cycle. The lifter mechanism raises the plate by a fixed amount,thereby causing it to pass the four spring-loaded latches, which retractas the plate is raised by the lifter. Once the bottom of the plate isabove the top of the latch, the latches are released, and a spring oneach latch causes the latch to extend under the plate. The liftermechanism then is lowered, causing the plate to be captured by the nowextended latches. The up-stacked plate thus is added to the bottom ofthe output stack.

[0127] b. General Attributes of the Latch Mechanism

[0128] The latch mechanism may be configured to have a low inherentsensitivity to the exact size, shape, construction material, and surfacefinish of the plate. For example, the four inwardly sloping, tapered (orangled) latches may cause the stack of plates to self-center within theplate-input area to accommodate both relatively small and large platesizes. Moreover, the mechanism may drop the plate gently onto the lifterwhen the singulation mechanism disengages from the edges of the plate,so that the plate may be lowered to the intrasite driver withoutspilling fluid from the wells. Moreover, if the ends of the latches aresufficiently smooth, the latches should not exert enough frictionalforce on the edges of the plate to cause the plate to tilt or otherwisehang up as the lifter mechanism is lowered and the plate is placed onthe intersite driver. A flexible latch mechanism is important because itfacilitates use of a wider variety of plates and other sample holderswith a reduced likelihood of failure. The depicted mechanism isespecially suited for use with the microplates described above.

[0129] The lifters associated with the latch mechanism generally may beactivated using any suitable mechanism. In the depicted embodiment, thelifters are activated using a spring and electromagnet. In alternativeembodiments, the lifters may be activated by gravity. In such analternative embodiment, the latches may pivot on their support pins suchthat their centers of gravity are offset. Consequently, when the liftermechanism is lowered, the latches are activated by gravity to return totheir nonretracted or extended state, thereby preventing the next platesin the stack from dropping as the lifter mechanism is lowered. If theoffset in the center of gravity of the latches is only enough to causethe latches to return to their extended positions, they should pressonly very lightly on the edges of the plate as it drops.

[0130] 2. Intrasite Drivers

[0131]FIG. 23 shows an intrasite driver 2300, which generally comprisesany mechanism for moving samples within an I/O and/or function ortransfer site, especially in cooperation with a latch or singulationmechanism. Intrasite driver 2300 includes a lift platform 2302 forraising and lowering plates and a drive mechanism 2304 for raising andlowering the lift platform.

[0132] Lift platform 2302 includes a base 2306 and sets of lifters 2308a,b corresponding to each I/O and/or function site. The liftersgenerally comprise any mechanism configured to raise or lower a plate incooperation with a singulation mechanism. Lifters 2308 a for use in theI/O sites are substantially rectangular and include a top notch 2310 forinteraction with a latch, as described above. Lifters 2308 b for use inthe function site are substantially cylindrical and may be used to raiseand lower a plate for transfer to a transport mechanism associated witha function module, as described below.

[0133] Drive mechanism 2304 includes a rotary drive motor 2320, an Acmescrew 2322, a slide 2324, a pair of opposed cam units 2326, and a pairof opposed guides 2328. These elements cooperate as described below toproduce a lifting force for raising and lowering lift platform 2302 andthus raising and lowering a plate. Here, rotary motion produced by motor2320 is converted to horizontal linear motion by Acme screw 2322, andthe horizontal motion is in turn converted to variable-rate verticalmotion by cam units 2326.

[0134] The rotary drive motor and Acme screw together form a linearactuator, which generally comprises any mechanism for producing a linearforce or displacement, including a positioning table, a rodlesscylinder, a robot module, an electric thrust cylinder, a pneumaticcylinder, a linear motor, a linear voice coil, and a solenoid. Here, therole of the rotary drive motor may be performed by any mechanism capableof producing rotary motion, including a motor, gear motor, gear reducer,manual hand crank, and micrometer, among others. Similarly, the role ofthe Acme screw may be performed by any mechanism capable of convertingrotary motion to linear motion. An Acme screw is a preferred mechanismfor converting rotary motion to linear motion because the Acme screwperforms this function using direct sliding friction, which helps tohold the load in position. In contrast, a belt drive or ball screw maypermit a load to back drive due to gravity when no torque is applied tothe motor. The Acme screw is an elongate structure that is connected ata first end through an intermediate pulley system 2330 to drive motor2320 and at a second end to slide 2324.

[0135] The cam units 2326 are substantially rectangular and include atop edge 2340, a bottom edge 2342, and a pair of opposed side walls2344. The side walls include two sloped drive channels 2348, whichfunction as the cams, and a vertical guidance channel 2350. A drive pin2352 is inserted through each drive channel 2348, and a guide pin 2354is inserted through the guide channel 2350. In alternative embodiments,pins and channels may be replaced with other components, includingridges, bearings, or rollers. Drive pins 2352 inserted into drivechannels 2348 are connected to slide 2324 on an inner side and to guides2328 on an outer side. In turn, slide 2324 is connected through the Acmescrew and pulley system to drive motor 2320, and the guides areconnected through the lift platform to lifters 2308 a,b. The drivermotor moves drive pins 2352 through drive channels 2348 between a topposition “A” closer to top edge 2340 and a bottom position “B” closer tobottom edge 2342. The drive pins are constrained to move horizontally,so that the pins push against an interior side 2356 of drive channels2348, urging cam unit 2326 to move both horizontally and vertically.Guide pins 2354 inserted into guidance channels 2350 are connected torelatively fixed portions of the transport module, preventing horizontalmotion, but permitting vertical motion, so that cam unit 2326 only movesvertically. As pin 2352 moves between positions A and B, the pin moves ahorizontal distance H and a vertical distance V. It is the verticaldisplacement that creates the raising and lowering motions. H and V maybe optimized for particular plates and travel distances; in transportmodule 2100, H and V are optimized for standard microplates and areapproximately 10 cm and 3.5 cm, respectively. Cam unit 2326 is raisedwhen drive pin 2352 is close to position A, and cam unit 2326 is loweredwhen drive pin 2352 is close to position B.

[0136] In use, a drive motor moves pins 2352 horizontally at asubstantially uniform rate; consequently, the slope of drive channel2348 determines the mechanical advantage and the rate of verticalmotion. Close to positions A and B, the slope of drive channel 2348 issubstantially zero, so that there is substantially no vertical motion.Stated differently, close to positions A and B, a preselected verticalposition corresponds to a range of horizontal positions. Thisconfiguration makes the vertical position relatively insensitive tomotor precision or manufacturing tolerance, because the lifter will beat the same vertical position whenever it simply is near positions A orB. Between positions A and B, the slope of drive channel 2348 isnonzero, so that there is vertical motion. The slope is largest(approximately 30°) between position A and an intermediate position “C,”so that the lifter raises and lowers relatively rapidly when it isfarthest from the bottom of the stack of plates. The slope is smallest(approximately 15°) between positions B and C, so that the lifter raisesand lowers relatively slowly when it is nearest to the bottom of thestack of plates.

[0137] The drive motor generally comprises any mechanism configured togenerate a driving motion, as described above. The drive motor used intransport module 2100 is a stepper motor, which generates a constanttorque. Generally, stepper motors and cams provide alternativemechanisms for performing the same function, in this case, generating avarying rate of motion. However, pairing a stepper motor and camtogether in the invention provides several advantages. In particular,the cam provides mechanical advantage and positional insensitivity, andpermits the stepper motor to be run at an optimal velocity profile. Ifthe stepper motor were used alone, a much larger motor would be requiredto produce the required forces. Conversely, if the cam were used alone,with a nonstepper motor, a system of limit switches would be required tolimit travel and provide positional feedback to release the latches.

[0138] 3. Intersite Drivers

[0139]FIG. 24 shows an intersite driver 2400, which generally comprisesany mechanism for moving samples between different I/O and/or functionsites. Intersite driver 2400 includes a tray 2402 for supporting a plateand a shuttle mechanism 2404 for moving the tray (and an associatedplate) between I/O and/or function or transfer sites. The tray mayinclude a substantially planar platform 2406 to support the plate and arim-like plate guide 2408 that partially surrounds the platform toposition and partially secure the plate. The tray also may includeapertures (or recesses) 2410 for passage of a lifter (such as lifters2308 a,b in FIG. 23) from an intrasite driver for use in raising orlowering plates supported by the tray. The shuttle mechanism includes amotor 2412, a pulley system 2414, a drive belt 2416, and a guide shaft2418. The motor is connected to the drive belt through the intermediatepulley system. The tray is connected to the drive belt and slidinglymounted about the guide shaft.

[0140] In use, the motor turns the intermediate pulley system, which inturn moves the drive belt, which in turn moves the tray, which movesalong a trajectory specified by the guide shaft. Suitable motors includeany mechanism for generating a force and/or torque, including but notlimited to a stepper motor. The tension in the drive belt may bemaintained using a tensioning spring attached to one end of the belt.

[0141] The transport module moves an input plate generally along an axis(e.g., an x-axis) from an I/O site to the transfer site and moves anoutput plate generally along the same axis but in the opposite directionfrom the transfer site to an I/O site. The input plate may be taken fromthe bottom of a stack of plates, and the output plate may be added tothe bottom of the same or a different stack of plates, as describedabove.

[0142] 4. Additional Features

[0143] The transport module may include additional features intended toenhance the convenience and/or functionality of the module, such asprocessing bins and barcode readers, among others.

[0144] The I/O sites in the transport module may accommodate a varietyof commercially available plates (e.g., microplates) and are largeenough so that the plates can be placed in the sites by a robot or ahuman hand. Moreover, as shown in FIG. 3, the I/O sites also mayaccommodate a variety of commercially available pre- and postprocessingplate bins (or magazines) for holding a stack of plates before and afteranalysis, respectively. A preprocessing bin may be removed from an I/Osite and replaced with another preprocessing bin containing a new stackof plates with samples to be analyzed. Similarly, a postprocessing binmay be removed from an I/O site and replaced with another postprocessingbin to receive a new stack of plates with samples that have beenanalyzed. The plate bins can be used with other robotics (such as anappropriate combination of function modules) to dispense, wash, and readwithout restacking plates. Preferred plate bins typically accommodatezero to sixty plates.

[0145] The transport module also may include barcode readers forautomatically identifying labeled plates. The barcode readers may bepositioned on different sides of the transfer site, so that the readerscan read barcodes mounted on different sides of a plate. The barcodereaders also may be positioned to reduce specular reflection. Thebarcodes preferably are read as plates are being raised, typicallyfollowing transport of the plate from an I/O site to the directtransporter access site. Barcode readers may be selected to read at 700scans per second or higher and be programmed to decode a variety ofsymbologies, including SPC (EAN, JAN, UPC), Code 39 (3-43 digits),Codabar (3-43 digits), Standard 2 of 5 (3-43 digits), Interleaved 2 of 5(4-43 digits), Code 93 (5-44 digits), and MSI-Plessey (4-22 digits),among others. Information obtained from the barcode can be used forvarious purposes. For example, the barcode can be used to conveyinstructions to the analyzer relating to required changes in assay modeor optics configuration. The barcode also can be used to name a reportfile.

5. EXAMPLES

[0146] The following examples illustrate the potential variety ofsingulation strategies available in a transport module having theindicated number of I/O sites and a capability for top and/or bottominput and/or output:

[0147] One I/O Site.

[0148] The transport module may take plates from the bottom or top of astack of plates at a single I/O site and add plates to the bottom or topof the same stack. There are four possible singulation strategies: BI/BOBI/TO TI/BO TI/TO

[0149] Here, B denotes bottom, T denotes top, I denotes input, and Odenotes output.

[0150] Two I/O Sites.

[0151] The transport module may take plates from the bottom or top of astack of plates in either I/O site and add plates to the bottom or topof the same stack in the same I/O site and/or another stack in the otherI/O site. There are sixteen possible singulation strategies: BI1/BO1TI1/BO1 BI2/BO1 TI2/BO1 BI1/TO1 TI1/TO1 BI2/TO1 TI2/TO1 BI1/BO2 TI1/BO2BI2/BO2 TI2/BO2 BI1/TO2 TI1/TO2 BI2/TO2 TI2/TO2

[0152] Here, 1 denotes site 1, 2 denotes site 2, and B, T, I, and O aredefined as above. Significantly, if there are dedicated input and outputsites, the transport module may (1) take plates from the bottom of thestack at the dedicated input site and add plates to the bottom of thestack at the dedicated output site, (2) take plates from the bottom ofthe stack at the dedicated input site and add plates to the top of thestack at the dedicated output site, (3) take plates from the top of thestack at the dedicated input site and add plates to the bottom of thestack at the dedicated output site, or (4) take plates from the top ofthe stack at the dedicated input site and add plates to the top of thestack at the dedicated output site.

[0153] Three or More I/O Sites.

[0154] The transport module may take plates from the bottom or top of astack of plates at any I/O site and add plates to the bottom or top ofthe same stack at the same I/O site and/or another stack at one of theother I/O sites. For a station with N I/O sites, there are generally(2N)² possible singulation strategies.

[0155] The singulation strategy used by a particular transport modulemay be fixed or varied from time to time or plate to plate. If there aretwo or more I/O sites, a given site may be used for input only, outputonly, or both input and output.

[0156] The I/O and function sites may be arranged to enhance convenienceand/or efficiency, for both human users and the function modules. Intransport module 2100, a first linear path connects the two I/O sitesand the transfer site, and a second substantially perpendicular linearpath connects the transfer site and the dispense and examination sites.However, the I/O and function sites also may be arranged in other ways.For example, the I/O, dispense, and examination sites all may bepositioned along a single substantially linear path, which may betraversed in a single direction if plates are input at one end of thepath and output at the other end of the path.

[0157] If there are separate input and output sites (or separate inputand output ends at a single I/O site), a robot may deliver a plate tothe input site and retrieve a (different) plate from the output site,both in the same trip. This feature is termed “process compression,”because it reduces robot hand travel in servicing the transport module.In contrast, if there is only a single input/output site (with deliveryand retrieval from the same side), the robot would have to remove anyanalyzed plates before delivering any unanalyzed plates. Thus, processcompression replaces two separate robot movements with one robotmovement.

C. Fluidics Module

[0158] The fluidics module generally comprises any mechanism or systemfor automatically dispensing fluid onto or into a sample holder. Themechanism may include reservoirs and dispense elements, and be capableof simultaneously and/or sequentially dispensing uniform and/ornonuniform fluid aliquots at one or more sample sites. The mechanismalso may include a thermal regulator to control fluid temperature,thereby reducing bubble formation. Further aspects of the fluidicsmodule are described in the following sections: (1) noncontact fluiddispensers, (2) contact fluid dispensers, (3) variable-pitch-array fluiddispensers, and (4) determination of inter-well separations.

[0159] 1. Noncontact Dispensing

[0160] Fluid may be dispensed using “noncontact dispensing,” whichgenerally comprises any mechanism capable of dispensing fluid withoutcontacting the fluid and/or sample container into which the fluid isdispensed. A simple example of a manual noncontact dispenser is aneyedropper, which can dispense drops of fluid without contacting asample or receptacle. Further aspects of noncontact dispensing aredescribed without limitation in the following examples:

a. Example 1 Positive-displacement Syringe Pump with Sapphire-tippedNozzles

[0161]FIG. 25 shows a noncontact fluid dispenser 3100 constructed inaccordance with aspects of the invention. Fluid dispenser 3100 mayinclude a fluid reservoir 3102, a pump 3104, and a dispense manifold3106 having at least one dispense element 3108.

[0162] Fluid reservoir 3102 generally comprises any container configuredto hold fluid for dispensing by dispenser 3100. Fluid reservoir 3102 maybe formed of any nonreactive material, including glass and variousplastics. Fluid reservoir 3102 may be configured so that it may beeasily replenished with fluid and/or easily replaced with an alternativefluid reservoir.

[0163] Pump 3104 generally comprises any device or mechanism configuredto move fluid between fluid reservoir 3102 and fluid manifold 3106, andto meter fluid accurately to dispense elements 3108. In FIG. 25, pump3104 includes a (positive-displacement) microstepping syringe pump 3110incorporating a plurality of syringes 3112 for dispensing fluid to aplurality of dispense elements 3108. The syringe pumps may operateindependently using separate actuators, or the syringe pumps may beganged together and driven using a single actuator. Using one or moreaspirate/dispense valves 3113, syringe pump 3110 may aspirate fluidthrough aspirating tubes 3114 from fluid reservoir 3102, and dispensefluid through dispensing tubes 3116 toward dispense manifold 3106.Aspirating tubes 3114 and dispensing tubes 3116 may include anymechanism for transporting fluid between a fluid reservoir, pump, anddispense manifold, including but not limited to hollow plastic tubing.

[0164] Dispense manifold 3106 generally comprises any support configuredto hold one or more dispense elements 3108. In FIG. 25, dispensemanifold 3106 is a substantially elongate bar that holds a linear arrayof dispense elements, which may be used to dispense fluid into a lineararray of sample holders, such as rows or columns in a microplate. Eachdispense element can be driven by a separate pump, or two or moredispense elements can be coupled hydraulically using a manifold anddriven by the same pump.

[0165] Dispense element 3108 generally comprises any element configuredto dispense fluid to a surface, sample holder, or other repository,including surfaces and other fluids, without contacting such surface,sample holder, or other repository. In FIG. 25, dispense element 3108includes (1) a receiving portion 3118 configured to receive fluid fromdispensing tube 3116, (2) an anchor portion 3120 configured to connectthe dispense element and dispense manifold 3106, and (3) a dispensingportion 3122 configured to dispense fluid received through dispensingtube 3116. Receiving portion 3118 generally includes a connector forconnecting and securing together dispensing manifold 3106 and dispenseelement 3108. Anchor portion 3120 generally is joined to dispensemanifold 3106 using some suitable mechanism, such as passing the anchorportion through an aperture 3124 in the dispense manifold. Anchorportion 3120 may be formed of various materials, including substantiallyrigid materials such as steel tubing to stabilize and reduce recoil ofthe dispense element during dispensing.

[0166] Dispensing portion 3122 generally includes an exit port such as anozzle 3126 through which dispensed fluid may exit the dispense element.The exit port may include a small cross-section orifice and/or a smalltapered tip and to increase the likelihood that dispensed fluid willexit the dispense element cleanly. The small cross-section orificeincreases the exit velocity of the fluid, enhancing the likelihood thatthe fluid has sufficient kinetic energy to overcome surface tension andinertia effects at low fluid volumes to separate cleanly from the tip.Alternatively, or in addition, the positive-displacement pump may beused to provide sufficient acceleration and exit velocity to the fluidto overcome surface tension, based on dispense volume, fluid viscosity,and other factors. The small and/or tapered tip reduces the surface areacapable of holding fluid, reducing the likelihood and potential size ofpendant drops. In FIG. 25, dispensing portion 3122 includes a200-micron-diameter sapphire orifice embedded in a dispense nozzle. Thedispense strategy also may include a suck-back feature to controlpendant drops and/or to increase predispense path length to allow ahigher exit velocity to be attained.

[0167] In an exemplary embodiment, the dispense element (3108) includesFEP tubing (3116) slid over a piece of metal tubing (3122) that has asapphire tip (3126) permanently embedded in an end. These elements aresurrounded by a machined tube with a large head (3120), which furthercompresses the FEP tubing and acts as a locational element in thedispense manifold (3106), setting the correct height and concentriclocation of the dispense element (3108). A screw-on fitting (3118)presses on the large head of the machined tube, pushing the dispenseelement (3108) into the tapped bore of the dispense manifold (3106),securing the dispense element in place.

[0168] Fluid dispenser 3100 may be used to dispense fluid to one or moresample holders. Generally, a sample holder may be positioned beneatheach dispense element, and pump 3104 may then be used to dispense ametered amount of fluid through each dispense element to each sampleholder. Sample holders may be identified and sample holders and dispenseelements may be aligned using any suitable mechanism. Each portion ofthis operation may be under computer control, including alignment of thedispense elements and sample holders, and operation of the pump, amongothers.

[0169] Fluid dispenser 3100 may be capable of dispensing fluids over awide range of fluid volumes, and particularly in a preferred rangebetween about 0.1 μL and about 100 μL. In assays, the coefficients ofvariation (CVs) for such dispenses preferably are about 2-10% or lessfor dispensed volumes down to about 0.1 μL. Fluid exit velocity may beoptimized for the dispensed volume, for example, to reduce splashing asthe fluid contacts the sample holder. The upper limit on dispense volumeis essentially unconstrained, except by pump capacity.

b. Example 2 Positive-Displacement Syringe Pump with Solenoid Valve andSapphire-Tipped Nozzles

[0170]FIG. 26 shows an alternative noncontact fluid dispenser 3150constructed in accordance with aspects of the invention. Fluid dispenser3150 generally includes a fluid reservoir 3152, a pump 3154, and adispense manifold 3156 having at least one dispense element 3158. Thesecomponents function essentially as described above for fluid reservoir3102, pump 3104, dispense manifold 3106, and dispense element 3108,respectively.

[0171] Fluid dispenser 3150 also includes a pulse element 3160, whichmay be used to create a pressure wave as the pulse element is opened andclosed to increase the energy of the fluid being dispensed. Pulseelement 3160 preferably comprises a solenoid valve mounted near thedispense element, and coupled to the dispense element via an inletfitting 3162. The pulse element may be pulsed or left open during thedispense. Each dispense element may be associated with its own pulseelement, or groups of dispense elements may share a pulse element. Eachpulse element may be under computer control.

C. Example 3 Positive-pressure Pump with Solenoid Valve andSapphire-tipped Nozzles

[0172]FIG. 27 shows another alternative noncontact fluid dispenser 3200constructed in accordance with aspects of the invention. Fluid dispenser3200 may include a pressure-responsive fluid reservoir 3202, a pressurepump 3204, and a dispense manifold 3206 having at least one dispenseelement 3208. Fluid may be dispensed from fluid reservoir 3202 todispense elements 3208 using one or more dispense tubes 3209.

[0173] Pressure-sensitive fluid reservoir 3202 generally comprises anycontainer configured to hold a fluid for dispensing, and to respond toan increase in pressure by dispensing a fluid. In FIG. 27,pressure-sensitive fluid reservoir 3202 comprises a fluid bladder, whichresponds to external pressure by decreasing in volume, concomitantlyextruding or dispensing fluid.

[0174] Pressure pump 3204 generally comprises any device or mechanismconfigured to apply a variable but controllable positive pressure topressure-sensitive fluid reservoir 3202. Pressure pump 3204 operates bycompressing pressure-sensitive fluid reservoir 3202, forcing fluid fromthe reservoir through dispense tube(s) 3209 to dispense elements 3208.In FIG. 27, pressure pump 3204 includes a pressure source 3210, anupstream pressure controller 3212, a pressure vessel 3214, and adownstream pressure controller 3216. Pressure source 3210 may includeany source of positive pressure, including a pump and/or a pressuretank, among others. Upstream pressure controller 3212 may include anymechanism for monitoring and/or regulating the pressure produced by thepressure source, and may be under manual or automatic control. Pressurevessel 3214 may include any container capable of enclosingpressure-sensitive fluid reservoir 3202 and maintaining a positivepressure on such reservoir. Downstream pressure controller 3216 mayinclude any mechanism for monitoring and/or regulating the pressure offluid in dispense tube(s) 3209.

[0175] Positive-pressure pumping preferably should be performed so thatadditional gases cannot go into solution in fluids being dispensed,because this could cause bubbles as the pressure is decreased duringdispensing. Such additional gases may be avoided as shown above by usingpreviously degassed fluids in a flexible bladder that is pressuredexternally in a pressure vessel.

[0176] Dispense manifold 3206 and dispense elements 3208 may takevarious forms, including forms described above for fluid dispensers 3100and 3150. In FIG. 27, a single dispensing tube 3209 is used to supplyfluid to the dispense elements 3208, and the dispense elements includepulse elements 3218, as described above. The pulse element is used tometer the fluid by timing the duration of the valve opening. Thisrequires the fluid to have a controlled and calibrated flow rate. Thepulse element also aids fluid dispensing, as described above, becausethe pressure wave aids fluid separation from the dispense element.

[0177] Alternative fluid dispensers may use alternative combinations ofcomponents. There may be a single pressure source for each dispenseelement, or there may be a common pressure source for sets of dispenseelements. There may be a single pulse element for each dispenseelements, or there may be a common pulse element for sets of dispenseelements. The pressure drop in the fluid after the pulse element foreach fluid path must be approximately the same for a common pulseelement. Single pulse elements for each dispense element may haveindividually calibrated open times or duty cycles during the open timeto account for differences in pressure drop.

d. Example 4 Positive-Displacement Syringe Pump with a Rectangular Arrayof PTFE Nozzles

[0178]FIG. 28 shows yet another alternative noncontact fluid dispenser3300 constructed in accordance with aspects of the invention. FIG. 28 isa schematic view of the fluid dispenser shown (together with a transportmodule and an analysis module) in FIG. 2 as part of an integrated systemfor preparing and/or analyzing samples. Fluid dispenser 3300 may includea fluid reservoir station 3302, at least one pump 3304, and at least onenoncontact dispense elements 3306. These components may functionessentially as described above in the context of FIGS. 25, 26, and/or27. In use, the pumps direct fluid from the fluid reservoir stationthrough the dispense elements and onto or into a sample holder such as amicroplate 3308.

[0179] Fluid reservoir station 3302 may include bottles or fluidcontainers 3310 for holding buffers, reagents, samples, or other fluidsfor use in a particular assay. Fluid containers 3310 may vary in size,depending on fluid requirements for a particular procedure. For example,a large container may be used to dispense a buffer used in manysequentially performed assays. Alternatively, a small container may beused to dispense a tracer used in relatively small quantities and/or ina relatively small number of assays. Fluid reservoir station 3302 may beconfigured to facilitate easy interchange of different fluid containersfor different purposes, for example, by using containers having asnap-on or screw-on connector. Fluid containers 3310 may be disposableor reusable and may be supplied independently or with a particular assaykit. The number of reservoirs that may be used simultaneously in station3302 may range from 1 to N, where N is the number of dispense elementassemblies that are connected to station 3302.

[0180] The dispenser effectively comprises an interchangeable conduitnetwork that allows any combination of dispense elements (or tipdevices) to be connected to any combination of fluid reservoirs.Dispenser 3300 may include one or more pumps 3304 such as syringe pumpsand one or more dispense elements 3306. Generally, any pump may beconnected to any fluid container, for example, via an aspiration tube3312. Thus, multiple pumps may be connected to one or some fluidcontainers, and no pumps connected to other fluid containers.Alternatively, each pump may be connected to a different fluidcontainer. Similarly, any pump may be connected to any dispense element,for example, via a dispense tube 3314. Thus, one pump may be connectedto one or multiple dispense elements, and so on. In a preferredconfiguration, the dispenser includes 32 separate syringe pumps 3304each connected one-on-one via separate dispense tubes 3314 to 32separate dispense elements 3306.

[0181] The syringe pump may include various drivers. For example, thesyringe pump may include a linear stepper motor or a linear servo motor.Alternatively, the syringe pump may include a rotary stepper motor or arotary servo motor.

[0182] Dispense elements 3306 generally may be organized in any suitablearrangement, including linear and rectangular arrays. In mostapplications, it is preferable to match the organization of the dispenseelements to the organization of all or part of the sample sites in thesample holder. Here, sample sites are preferred sample locations withinthe sample holder. Thus, a periodic (e.g., rectangular, hexagonal, etc.)arrangement of dispense elements is preferable for a sample holder suchas a microplate or biochip having a periodic array of sample sites. Inessence, the dispense elements are arranged to form an array of fluiddispensing channels that correspond to the sample sites. In a preferredconfiguration, the dispenser includes 32 dispense elements organized asa 4×8 regular array 3316, and more specifically as a 4×8 rectangulararray with 9 mm separations to correspond to the 9 mm well separation instandard 96-well microplates, as described above.

[0183] Dispense-element array 3316 may be used to dispense individualmeasured aliquots of fluid onto or into a sample holder. For example,the array may be used to dispense into some or all of the wells 3318 inmicroplate 3308 by aligning the array with the wells and dispensing. Ifthere are more sample wells than dispense elements, dispensing can occurin steps by dispensing to a first set of wells 3322, moving the dispensearray and microplate relative to one another (for example, along aY-axis), and then dispensing to a second set of wells 3324. This processmay be repeated for additional sets of wells 3326 as necessary. Thisprocess is illustrated in FIG. 28, in which three sets of dispenses froma 4×8 array are used to dispense into a 96-well microplate.

[0184] A similar process may be used to dispense fluid into a microplatethat has a higher density of wells, for example, 384-wells, or1536-wells, among others. This can be accomplished by offsetting thedispense element array 3316 and/or microplate 3308 in the X directionand doing numerous passes in the Y direction. For example, two fullpasses in the Y direction with one adjustment in the X direction willallow dispensing in each well of a 384-well microplate. Similarly, fourfull passes in the Y direction with three adjustments in the X directionwill allow dispensing in each well of a 1536-well microplate. Theadjustment or offset should be by an integer multiple of thewell-to-well spacing. Dispensing by column into 96, 384, 864, 1536, and3456 well microplates can be accomplished using a linear array of 8dispensing tips, since the number of rows is 8, 16, 24, 32, and 48,respectively. Dispensing by row into 96, 384, 864, 1536, and 3456-wellmicroplates can be accomplished using a linear array of 12 dispensingtips since the number of columns is 12, 24, 36, 48, and 72 respectively.Any microplate with a number of columns or rows that is divisible by 8can be dispensed into with this method. A rectangular array ofdispensing tips may also be used with the center-to-center spacing of 9mm in both directions, since the well-to-well spacing in all theabove-mentioned plates is 9 mm or an integer fraction thereof (e.g., 4.5mm, 2.25 mm, etc.).

[0185]FIG. 29 shows a portion of fluid dispenser 3300 including adispense driver 3400 and an array 3402 of dispense elements 3404positioned above a microplate 3406 at a dispense site. (The distancebetween the dispense driver and microplate has been exaggerated forclarity.) FIG. 29 is a partial view of fluid dispenser components shownin FIGS. 2, 3, and 18 relative to transport and/or analysis modules. Thefluid dispenser generally may include (or associate) registrationmechanisms for moving the dispense array and/or the microplate or othersample holder relative to one another along X, Y, and/or Z axes fordispensing. Such movement may be effected using any suitablecombination(s) of drive mechanisms and any suitable drive strategy. Influid dispenser 3300, the microplate is moved relative to the dispensearray along the X and Y axes, and the dispense array is moved relativeto the microplate along the Z-axis. More specifically, the microplate ismoved using a transporter shared with an analysis module, as describedbelow in connection with the analysis module, and the dispense array ismoved using dispense driver 3400.

[0186] Dispense driver 3400 includes a linear actuator 3410 and parallelslides 3412 a,b directed along the Z-axis on opposite sides of array3402. The actuator moves the dispense array along the Z-axis guided bythe parallel slides, so that the array may be raised and loweredrelative to the microplate. Here, the linear actuator includes a steppermotor 3414 and an Acme screw 3416, although any mechanism capable ofgenerating a linear displacement may be used, as described above inconnection with the intrasite driver used in the fluidics module.

[0187] The array of dispense elements generally may be formed from oneor more banks 3420 of dispense elements. In fluid dispenser 3300, thesebanks each include 8 dispense elements, which may be driven directly bya positive displacement pump or by a manifold. The banks may bepositioned near one another with a spacing corresponding to the spacingbetween integer numbers of sample sites, for example, about 9 mm forstandard microplates. This spacing may reduce spatial requirements whilepreserving an ability to dispense into the entire microplate. Thisspacing also may permit dispensing of multiple reagents with one scan ofthe sample holder under the dispenser array.

[0188] Each bank of dispensers can be independently installed orde-installed into a standard slot arrangement. With this slotarrangement, banks of dispense tips with different dispensecharacteristics (e.g., number of tips, volume range, or other functionssuch as plate washing) may be installed in a mix and match fashion.Software can be configured for the type of module that has beeninstalled into each slot, and programmed accordingly. For example,microplate washing can be implemented by changing the design andprogramming of each bank of dispense elements. With proper design andsizing, one bank of dispense elements can aspirate solution from acolumn or row of wells, while another bank can subsequently dispenseclean solution. Alternately, for the wash function, a head may containboth dispense and aspirate elements, at different heights, allowingdispense and aspirate without movement of the plate.

[0189] When each dispense element is connected to a separate pump, asoftware program can control the pumps while the plate is being scannedto allow random access dispensing of any reagent into any well. Inparallel dispensing or transfer systems (e.g., pin transfer devices orarrays of conventional pipettes), random access is only possible if asource plate is first created with the desired reagent distribution orif the reagents somehow can be routed into the tops of the pipettes fromseparate sources. The dispenses from each dispense element may beperformed simultaneously or sequentially, and be of uniform ornonuniform aliquots.

[0190]FIG. 30 shows a fluid control unit 3400 for use with the fluiddispenser of FIG. 28; alternative views/embodiments are shown in FIGS. 2and 3 in relation to optionally associated transport and analysismodules. The fluid control unit generally comprises the pump or pumpsand associated drivers used to direct fluid from a fluid reservoirstation to one or more dispense elements. Fluid control unit 3400includes a plurality of pumps 3402 (such as syringe pumps) andassociated drivers 3404 mounted in a chassis 3406. The syringe pumpsinclude a syringe 3410 and an inlet/outlet valve 3412. The syringe isused to aspirate and dispense fluid and includes a barrel 3414 forholding fluid and a plunger 3416 slidably received within the barrel andcapable of generating a positive displacement. The plunger may beoperatively connected to driver 3404. The valve is used for fluidinput/output and includes an inlet 3418 for connecting to an aspirationor input tube 3419 coming from a fluid reservoir and an outlet 3420 forconnecting to a dispense or output tube 3421 going to one or moredispense elements. Fluid reservoirs may be placed adjacent the fluidcontrol unit to provide convenience in operation.

[0191] The valve or associated pump may include labels 3422 to assisthookup of input and output tubes. For example, valves and/or pumpsassociated with a control unit for a 4×8 array of dispense elements maybe labeled A1-H1, A2-H2, A3-H3, and A4-H4, where the A-H are thestandard designators for the 8 rows in a standard 96-well microplate,and the 1-4 refer to four columns. Moreover, valves, pumps, and/orinput/output tubes, or portions thereof, may be color-coded, forexample, using red, yellow, blue, and green to denote 1-4, as definedabove. Generally, any marking or component capable of distinguishingvalves, pumps, and/or tubes may functions as markings; however,preferred markings are number and/or letter codes and colors.

[0192] A preferred syringe pump is a CAVRO syringe pump. The startingspeed of the CAVRO syringe pump is 1000 ½ steps/second, and theassociated acceleration (slope) is 50,000 ½ steps/second². The pumpexecutes 6000 ½ steps in its 30-mm travel, so that its starting speed is5 mm/second, and its associated acceleration is 250 mm/second². If usedwith a 500-μL syringe, there are about 12½ steps per μL, so that thestarting speed and top speed are not too different with the relativelysmall volumes (e.g., 0.5 μL) used here.

[0193]FIG. 31 shows a bank of dispense elements 3500 for use with thefluid dispenser of FIG. 28. The bank includes a manifold 3502 and aplurality of substantially equally spaced dispense elements 3504 eachattached to a tubing assembly 3506. The manifold supports the dispenseelements and may be used to affix the bank to a dispense driver usingsuitable affixing means, such as fasteners 3508. The manifold may beformed of any suitable material, such as stainless steel, which isresistant to fluids and other materials that may come into contact withthe manifold. The manifold may be asymmetric to ensure that it ismounted properly at a dispense site. The tubing assembly is used toconnect the dispense elements to the fluid reservoir(s). The manifoldand/or tubing assemblies may include labels 3510 a,b,c to assist hookupbetween the manifold and assemblies.

[0194]FIGS. 32 and 33 show alternative views of bank 3500 and associatedtubing assemblies 3506. The tubing assembly may include an input(distal) flange 3520 for connecting to a pump (e.g., in a fluid controlunit), an output (proximal) flange 3522 for connecting to a dispenseelement, and a section of tubing 3524 for spanning the gap between thepump and the dispense element. The input and output flanges generallycomprise any suitable mechanism for ending the tubing so that it may bejoined to another structure. For example, the flanges may include{fraction (1/4)}-28 fittings. The tubing generally may have any suitabledimensions. For example, the tube may be about 40 inches long toaccommodate positioning of the pumps relative to the dispense array,with an inner diameter of about {fraction (30/1000)} of an inch and anouter diameter of about {fraction (62/1000)} ({fraction (1/16)}) of aninch. The tubing further may include reinforcements such as a spiralwrap strain relief 3526 positioned adjacent the output flange. Apreferred tube material is FEP. The dispense element may include a head(or tip flange) 3530, a body tube 3532, and a dispense tip 3534. Thetubing assembly and an associated dispense element may be operativelyjoined by inserting both into an appropriately sized aperture 3540 inmanifold 3502, separated by washers 3542 a,b and an intervening O-ring3544.

[0195] The fluid enters the dispense element at the interface of the tipflange and supply tubing flange. This flanged interface may reduce fluidholdup and dead volume areas, important when changing fluids or cleaningthe tip, and may allow for either the tip or supply tubing to be changedindependently. The tip flange may be formed via a machined PEEK plasticsection of the tip. The tubing flange may be formed conventionally. Thismachined flange is press-fit onto a stainless steel tube. The entireinner surface of the PEEK flange and stainless steel tube is lined withthin-wall PTFE heat-shrink tubing, terminating at the PEEK flange at oneend and the dispense nozzle 3550 at the other (dispense) end. Thedispense end is formed from the heat-shrink tubing into a cone-shapednozzle protruding from the stainless steel tubing. The thin wall of theheat-shrink tubing and its ability to shrink onto a mandrel areimportant features of the dispense element. The cone-shaped nozzle maybe formed manually. This process should be performed carefully andreproducibly, since a burr on the dispense end, an unsquare cut of thedispense end, or a slightly misshaped nozzle all may affect dispensingperformance. Alternatively, the dispense element may include aconventionally injected molded tip made of polypropylene withsubstantially similar geometry. The wall thickness and aperture openingwould be of similar size, and care would have to be taken to ensure thatno flash from the molding process affected dispensing performance.

[0196] The noncontact flanged dispense tip described here shares manyfeatures with the sapphire dispense tip described above, including asmall, controlled, inner-diameter bore and a small-to-minimum surfacearea at the dispense end of the tip. The inner diameter of the orificeof the noncontact flanged dispense tip is about 190±10 microns, and theinner diameter of the orifice in the sapphire tip is about 200 microns.The circumferential wall of the tip around the dispense orifice is about5-thousandths of an inch thick. The small bore increases the exitvelocity of the fluid, and the minimum surface area decreases surfacetension, both of which are important for cleanly ejecting small (˜0.5μL) drops of fluid. The noncontact flanged dispense tip also provides acompletely nonmetallic flow path because the interior of the flow pathis PTFE Teflon. This greatly reduces the formation of pendant drops dueto the surface properties of the Teflon, which is an improvement overthe design of the sapphire tip. Generally, any material (such as ahydrophobic material) that reduces the affinity of the dispensed fluidfor the dispense element may be used within the fluid path and/or at thedispense tip to reduce pendant drops. Such materials includepolypropylene, polyethylene, and FEP.

[0197] The system described above may be used to dispense fluid volumesdown to 0.25 μL or less. Small (submicron) volumes generally may bedispensed by decreasing the thickness of the wall of the tip, especiallyto or below about 8-thousandths of an inch, and even to or below about2.5-thousandths of an inch. Generally, a wall thickness of about10-thousandths of an inch does not work well for dispensed volumes ofless than about 1 μL. Smaller dispensed volumes also may be obtained byusing a syringe pump with a linear motor, which may also increase therate of fluid dispensing by providing a more rapid acceleration and thusa higher exit velocity.

[0198] In summary, the noncontact dispenser may include a fluid source,a pump, and a noncontact dispenser, where a conduit path extends fromthe pump to the orifice of the dispenser. The conduit path may remainopen and unconstricted between successive depositions because fluid isretained in the conduit path by surface tension and/or capillary actionuntil expelled by the positive displacement pump. Thus, the dispensermay dispense fluid without closing or constricting the conduit channel,or contacting droplets of the dispensed fluid to a surface. Moreover,the rate of deposition will generally correspond to or equal theincremental rate of pumping. The dispenser may be used to deposit fluidaliquots as small as 5 μL or less.

[0199] 2. Contact Dispensing

[0200] Fluid also may be dispensed by “contact dispensing,” whichgenerally comprises any mechanism for dispensing fluid in which thedispenser contacts the sample and/or sample container into which thefluid is dispensed. An example of a contact dispenser is a pin transferdevice, which uses a pin to pick up small quantities of fluid from astorage area and transfer the fluid to a receptacle. Pin transferdevices are described below in the context of microplates, although theyalso may be used for transfer to and/or from other sample containers.Further aspects of contact dispensing are described without limitationin the following examples:

a. Example 1

[0201]FIG. 34 shows a pin transfer device 3700. Pin transfer device 3700includes a pin 3702 and a mount 3703 configured to support the pin sothat a tip 3704 of the pin is presented for fluid transfer. Pin transferdevice 3700 may be used to transfer a small amount of a first liquid3706 from a storage area 3708 to a second liquid 3710 in a receptacle3712. This transfer may proceed in two steps:

[0202] Step 1. For loading, pin transfer device 3700 is positioned overstorage area 3708 (Panel A), lowered until tip 3704 contacts firstliquid 3706 (Panel B), and then raised until tip 3704 breaks contactwith first liquid 3706 (Panel C). In the process, a drop 3714 of firstliquid 3706 remains in contact with tip 3704 due to surface tension.

[0203] Step 2. For dispensing, pin transfer device 3700 is positionedover receptacle 3712 (Panel D), lowered until tip 3704 and drop 3714contact second liquid 3710 (Panel E), and then raised until tip 3704breaks contact with second liquid 3710 (Panel F). In the process, drop3714 will be transferred to second liquid 3710. (A new drop 3716representing a mix of second liquid 3710 and drop 3714 may remain incontact with tip 3704 after the transfer.).

[0204] The volume of drop 3714 will depend on various factors, including(1) the surface tension and viscosity of first liquid 3706, (2) thematerial, geometry, and cleanliness of tip 3704, and (3) the kinetics oftransfer. However, for a fixed set of parameters (e.g., fluid, tip,etc.), the volume should be relatively precise and reproducible,permitting volumetric fluid transfer.

b. Example 2

[0205]FIG. 35 shows an alternative pin transfer device 3750. Pintransfer device 3750 includes a plurality of pins 3752 and a rigid mount3754 configured to support the pins in a preselected array. The tips3756 of pins 3752 lie approximately within a plane 3758. Pin transferdevice 3750 is configured to transfer a drop of fluid 3760simultaneously between arrays of storage areas and/or receptacles, suchas wells 3762 in a microplate 3764. More specifically, the device isconfigured to transfer fluid substantially simultaneously betweenstorage areas and receptacles by substantially simultaneously contactingthe pins to the storage area(s) to load the fluid, and thensubstantially simultaneously contacting the loaded pins to thereceptacle(s) to unload the fluid.

[0206] Unfortunately, pin transfer devices using a rigid array of pinsmay suffer from a number of shortcomings. For example, there may bevariations in the dispensed volume if the receptacles do not lie in asingle plane, because the tips of some of the pins may not be able tocontact the associated receptacle. There also may be variations in thedispensed volume if the receptacles are unevenly spaced perpendicular tothe plane of the tips, because some of the pins may miss the associatedreceptacle. These shortcomings may be particularly acute for transfer toand/or from microplates, because microplates may vary in theirdimensions due to shrinkage or expansion during or after molding andbecause microplate wells may have uneven bottom surfaces.

C. Example 3

[0207]FIGS. 36 and 37 show another alternative pin transfer device 3800configured to transfer fluid simultaneously between arrays of storageareas and/or receptacles. Pin transfer device 3800 includes a pluralityof pins 3802 and a flexible mount 3804 configured to support the pinssecurely but movably in a preselected array. The flexible mount mayallow the pins to move vertically and/or horizontally relative to theirequilibrium positions. In pin transfer device 3800, flexible mount 3804includes a rigid block 3806, a film 3808 abutting the rigid block, aflexible (or elastomeric) sheet 3810 abutting the film, and a holder3812 abutting and at least partially holding the block, film, and sheet.Pins 3802 are embedded in flexible sheet 3810 and slidably positionedthrough apertures 3814 in film 3808 and rigid block 3806. Portions ofthe pins configured to contact the flexible sheet may be etched tofacilitate adhesion with the sheet. Rigid block 3806 provides structuralrigidity that maintains the orientation and relative positions of thepins. Film 3808 separates rigid block 3806 and flexible sheet 3810,permitting the flexible sheet to move independently of the rigid block.Flexible sheet 3810 provides a force that biases pins 3802 toward rigidblock 3806. Flexible sheet 3810 may include one or more layers,providing a flexible and chemical-resistant surface and the desiredcompliance and mechanical stability. Film 3808 and/or flexible sheet3810 may provide a barrier to fluid flow through the device. Pintransfer device 3800 may be used to transfer fluid to a microplate 3820having a plurality of wells 3822.

[0208] A flexible mounting mechanism may overcome shortcomingsassociated with rigid mounts. For example, a flexible mechanism mayallow pins to move rather than bend or break if accidentally broughtinto contact with a surface such as a shallow well bottom during fluidtransfer. A flexible mechanism also may be used to compensate forvariations in sample-holder dimensions, such as variations due toshrinkage and/or expansion relative to the “nominal” dimensions. Forexample, the flexible sheet may be mounted in a frame whose outerdimensions can be adjusted to be slightly larger or slightly smallerthan the nominal dimensions, for example, by placing the sheet understress. The pin-to-pin spacing can then be reduced to match a smallersample holder by decreasing the stress on the sheet (e.g., by adjustingthe outer frame), and increased to match a larger sample holder byincreasing the stress on the sheet.

[0209] The flexible mounting mechanism in pin transfer device 3800 mayovercome shortcomings associated with other flexible mounts, such asflexible mounts that simply permit pins to float in their mounts. Forexample, the flexible sheet may inhibit the accumulation of solids onthe pins near the anchor points of the pins, reducing friction betweenthe pins and their fixtures. Such friction may prevent the pins frommoving freely or at all, so that some pins may not be able to touch thedesired surface and transfer fluid uniformly. The sheet also mayfacilitate cleaning, because the ends of the pins are sealed in thesheet, reducing contamination by cleaning materials. Typically, thedevice is cleaned by immersing and/or scrubbing portions of the devicethat contact fluid, such as the tips of the pins, with a cleaning fluid.

[0210] Pin transfer device 3800 generally may be formed or constructedusing any suitable technique, including the following five-step process.First, pins 3802 may be positioned in a rack. Second, pins 3802 may bepositioned through rigid block 3806 and film 3808. Third, flexible sheet3810 may be poured to encapsulate the pins, and allowed to dry. Fourth,holder 3812 may be mounted to the sandwich formed by the rigid block,film, and flexible sheet. Finally, the finished device may be removedfrom the rack.

[0211] Pin transfer device 3800 also generally may be formed of anymaterials having the desired mechanical properties. For example, theflexible sheet may be formed of any suitable flexible material, and thepins may be formed of any suitable wetable material that facilitates theloading and unloading of reproducible volumes of fluids. Preferredmaterials include a silicone RTV sheet and a closed cell polyurethanefoam for the mount and stainless steel for the pin.

[0212] The pin transfer device may be used manually and/orautomatically. For example, pin transfer device 3800 includes apertures3830 for mounting the device to a driver for raising and lowering thedevice relative to a sample, and/or for moving the device betweendifferent samples.

[0213] The pin transfer device also may be used in conjunction with anysuitable sample holder, including microplates. If used with amicroplate, the pin transfer device may include linear or rectangulararrays of pins corresponding to some or all of the rows or columns in amicroplate having 96, 384, 864, 1536, 3872, 9600, or another number ofwells. In turn, the microplate or other sample holder may be constructedto transfer information regarding the form of the microplate to the pintransfer device. Such information may include the dimensions of thesample holder and the number and dimensions of any associated samplewells. Such information may be encoded using a bar code, a referencefiducial, and/or other features of the sample holder.

[0214] 3. Variable Pitch Array Fluid Dispenser

[0215] The separations between dispense elements in a fluid dispensermay be fixed to correspond to nominal separations between sample sitesin standard sample holders, or integer multiples thereof, as describedabove. However, if the separations between sample sites in actual sampleholders differ significantly from the nominal separations in thestandard sample holders, these fluid dispensers may dispense fluid ontothe side or outside of the intended sample sites in the sample holder.Such misdirected dispenses may be especially likely with microplatesample holders, because microplate dimensions often vary due toshrinkage and/or expansion during or after molding. To overcome thesedifficulties, the fluid dispenser may include mechanisms for actuallyand/or effectively adjusting the separation between dispense elements tomatch the separation between sample sites in a given sample holder.

[0216]FIGS. 38 and 39 show a variable-pitch-array fluid dispenser 3900that may be used effectively to adjust the separation between dispenseelements. Fluid dispenser 3900 includes a dispense manifold 3902 and adispense site 3904 configured to receive a sample holder 3906 having aplurality of sample wells 3908.

[0217] Dispense manifold 3902 may take various forms. For example,dispense manifold 3902 includes a substantially linear array of dispenseelements 3910. The manifold includes a fluid inlet 3912 positionedadjacent a first end 3914 of the array and a pivot 3916 positionedadjacent a second end 3918 of the array. Fluid inlet 3912 is operativelyconnected to dispense elements 3910, so that fluid may enter dispensemanifold 3902 through fluid inlet 3912 and exit dispense manifold 3902through dispense tips 3920 of dispense elements 3904. Fluid 3922 may bedispensed through dispense tips 3920 using a variety of mechanisms,including noncontact mechanisms, as described above. The fluid may exitthe dispense tip in various forms, including drops, trains, and streams,among others, depending on exit velocity, dispense duration, orificediameter, and so on.

[0218] Dispense manifold 3902 is rotatable about pivot 3916, so that theeffective separation between dispense elements 3910 can be adjusted tomatch the actual separation between sample wells 3908 in sample holder3906. Specifically, dispense manifold 3902 may be rotated relative to asample holder, so that the array of dispense elements is oriented at anangle θ relative to the array of sample wells. Rotation of the array ofdispense elements relative to the sample holder effectively decreasesthe separations between dispense elements relative to the sample holder.Mathematically, the effective separation between linearly arrayeddispense elements is described by the following equation:

S _(eff) =S·cos θ  (1)

[0219] Here, S_(eff) is the effective separation between dispenseelements, S is the actual separation between dispense elements, and θ isthe angle between the array of dispense elements and the array of samplewells. Generally, the actual separation between dispense elements in thedispense manifold should equal or exceed the maximum separation betweensample wells in expected sample holders, because relative rotation ofthe dispense manifold and sample wells can only decrease the effectiveseparation between the dispense elements.

[0220] Rotation of the dispense manifold about the pivot generally maybe controlled automatically by the dispenser or manually by an operator.If the pivot is controlled automatically, a driver may be connected tothe pivot or to the dispense manifold, depending on whether the dispensemanifold is attached fixedly or rotatably to the pivot, respectively.

[0221] Fluid is dispensed into a sample holder by adjusting the relativepositions of the dispense elements and sample holder so that S_(eff) issubstantially equal to the actual separation between sample sites, andthen by moving the sample holder relative to the dispense site whilesimultaneously or sequentially dispensing fluid from the dispense tipsof the dispense elements. Fluid may be dispensed simultaneously if theangle of rotation θ is small, so that each dispense element ispositioned over a sample well simultaneously. Fluid may be dispensedsequentially if the angle of rotation θ is large, so that only somedispense elements are positioned over a sample well at a given time. Inthe latter case, fluid dispensing must be coordinated with the relativemotion of the sample holder. If the sample holder includes multiple rowsof sample wells, fluid may be dispensed sequentially into each rowthrough cycles of motion and dispensing, the cycles of relative motionbringing subsequent rows of sample wells into alignment with thedispense manifold. Generally, the sample holder may be moved, thedispense manifold may be moved, or both may be moved for fluiddispensing.

[0222] The relative positions of the sample holder and dispense site maybe altered using any suitable mechanism. For example, the dispensemanifold may be rotated and/or translated relative to the sample holder,the sample holder may be rotated and/or translated relative to thedispense manifold, or the sample holder and dispense manifold may berotated and/or translated relative to one another. Similarly, thedispense manifold and/or the sample holder may be rotated about avariety of positions, so that the pivot may be located at variouspositions within the dispense manifold and/or dispense site.

[0223] Alternative mechanisms also may be used to adjust the separationbetween dispense elements in a fluid dispenser to correspond to theseparation of sample wells in a sample holder. In one alternative, theseparation between each pair of dispense elements may be adjusted tocorrect for deviations in positions of sample wells along a first axis,and the relative distance moved by the fluid dispenser and sample holdermay be adjusted to correct for deviations in positions of sample wellsalong a second axis. In another alternative, if each dispense elementcan be individually controlled, a linear array of dispense elements andsample wells may be moved parallel to one another, coordinating thedispensing of fluid with the motion. This requires closely coordinatingdispensing and motion, and is essentially a group of single dispenses.In yet another alternative, each linear array in a rectangular array ofdispense elements may slide relative to one another, so that elements ineach linear array may rotate and translate to establish and maintainalignment with rows of sample wells.

[0224] The variable-pitch array fluid dispenser generally may be usedwith various sample holders and various types of dispensing. Forexample, the dispenser may be used with microplates and surfaces.Similarly, although the dispenser was described primarily in the contextof noncontact fluid dispensing, aspects of the invention could be usedto position a contact (e.g., pin transfer) fluid dispenser relative tosample wells in a sample holder.

[0225] 4. Determination of Inter-well Separations

[0226] The fluid dispenser also may include mechanisms for determiningthe separation between sample positions in a sample holder, and forcommunicating these separations to an operator and/or an automatedcontroller. These mechanisms may be used to position a sample holderrelative to a fluid dispenser, and/or to position a sample holderrelative to other devices, such as excitation and/or emission elementsin a light detection device. FIGS. 38-39 show several of thesemechanisms.

[0227] Sample positions may be determined using any mechanism capable ofmeasuring positions, either before or during fluid dispensing.Information regarding sample positions may be determined before fluiddispensing by inspecting individual sample holders, or by inspectingrepresentative sample holders in a batch of sample holders. The latterapproach would be most successful if plate-to-plate variations withinthe batch are small. Information regarding sample positions may beprovided to a controller for the dispenser or other device, eithermanually or automatically. For example, information could be enteredmanually by an operator, as at a keyboard. Alternatively, informationcould be entered automatically by encoding the information on the sampleholder and then reading the information prior to dispensing. Forexample, information could be entered using a bar code 3930 on thesample holder and a bar code reader associated with the dispenser.

[0228] Information regarding sample positions also may be determinedimmediately before or during fluid dispensing by inspecting individualsample holders. One method for determining sample positions is to use animaging device 3932, such as a camera, and image recognition software toidentify the actual location of sample positions. Another method is touse a light detection or other device to locate reference fiducials 3234associated with the sample holder, and to identify the positions ofsample wells from the positions of reference fiducials by interpolationand/or extrapolation. Such reference fiducials could include dedicatedfeatures, and/or specific sample positions or edges of the sampleholder, among others, as described in PCT Patent Application Ser. No.PCT/US99/08410, filed Apr. 16, 1999, and incorporated herein byreference.

[0229] Information regarding positions of sample wells may be used byvarious function modules, including a fluidics module, as here, or ananalysis module, as described below.

D. Auxiliary Modules

[0230] This section describes auxiliary function modules that may beused alone as stand-alone units or together with or in lieu of fluidicsand/or analysis modules in an integrated system for sample preparationand/or analysis. An auxiliary module generally comprises any mechanismor system for performing functions that complement or assist fluiddispensing and/or analysis. Exemplary auxiliary modules include amongothers (1) a cleaning module, (2) a sample-containment module, and (3)an incubation module.

[0231] 1. Cleaning Module

[0232] A cleaning module generally comprises any mechanism or system forcleaning a sample holder such as a microplate. A cleaning module (orcleaning function) may be integrated with a fluidics module, forexample, by alternately aspirating and dispensing cleaning and rinsingfluids with the dispense elements. Alternatively, a cleaning module maybe a stand-alone system, for example, having a washer, a dryer, and anoutlet.

[0233] The washer is used to wash a sample holder using any suitablemechanism or method. Washing comprises removing sample or otherimpurities. Typically, the washer cleans a sample holder by spraying,immersing, scrubbing, or otherwise sequentially applying cleaning andrinsing fluids to the sample holder. The sample holder is cleaned ofsample using the cleaning fluid and rinsed of cleaning fluid (and anyresidual sample) using the rinsing fluid. The cleaning and rinsingfluids may be identical. The washer may include apparatus for fluidcleaning such as reservoirs and nozzles, and apparatus for contactcleaning such as scrubbers.

[0234] The dryer is used to dry a sample holder using any suitablemechanism or method. Drying comprises removing any rinsing fluidremaining after washing. Typically, the dryer dries a sample holderusing forced air (or other gas), heat, and/or agitation, among others.The dryer may include apparatus for forcing air such as a gas tank,compressor, and/or nozzle, as well as apparatus for heating and/oragitating such as a heating element or spinner. In some systems, dryingmay consist simply of room-temperature air drying.

[0235] The outlet is used to eliminate discarded sample, and cleaningand rinsing fluids, using any suitable mechanism or method. Typically,the outlet comprises a drain and/or a reservoir.

[0236] 2. Sample-Containment Module

[0237] FIGS. 40-43 show a sample-containment module constructed inaccordance with aspects of the invention. The containment modulegenerally comprises any mechanism or system for sealing wells or otherreservoirs in a sample holder. The mechanisms may include temporarilyapplying a sealing sheet to the top of the sample holder and/or removinga sealing sheet prior to dispensing fluid and/or analyzing a sample. Thesample holders including microplates may be of a standard design or of acustom design especially intended to work with a particular cover.Aspects of the invention may include (1) cover materials for sampleholders, (2) suitably covered sample holders, (3) systems forautomatically applying and/or removing covers from sample holders,and/or (4) systems integrating a sample-containment module with atransport module and/or other function modules.

[0238] A sample-containment module may be useful in solving problemsassociated with microplates and other sample holders, particularly forhigh-throughput applications. For example, microplates include wellshaving an open face that permits cross-contamination and evaporation.Therefore, it sometimes is desirable to seal the wells in a microplateto isolate the contents of each well from other wells and from theambient environment. One or both of these functions may be performed inprincipal by a microplate cover. However, microplate covers that havebeen used in the past have problems that make them unsuitable for use ina highly automated laboratory setting. In particular, past microplatecovers may interfere with or prohibit the stacking and/or unstacking ofmicroplates, due to spatial constraints or limitations in the specialhandling equipment used to stack and unstack the microplates. Moreover,microplate covers may permit gas exchange, facilitating evaporation. Inaddition, microplate covers or seals that use adhesive may be difficultto remove or may leave adhesive residue on a surface of a microplate,such that the microplate could stick to other microplates if stacked,unstacked, or otherwise contacted.

[0239]FIG. 40 shows a microplate 4110 and a sealing sheet 4112 coveringsample wells (not shown) in the microplate. Rectangular sealing sheets4113 may be applied to respective microplate tops from an input roll4114 and/or removed and transferred from microplate tops to an outputroll 4116, where they can be stored prior to disposal. Generally,sealing sheets may be stamped and carried on continuous input/outputrolls much like industry standard labels. The rolls can be loaded intoautomated application (sealing) and removal (de-sealing) machinesconfigured to operate with standard and/or specially designedmicroplates. Stacks of microplates may be fed into application/removalmachines, and seals may be applied or removed as desired. Typically, asealing sheet will be applied to a microplate (or other sample holder)before incubation and/or storage, and removed from a microplate beforefluidics operations and/or sample analysis.

[0240] Sealing sheets may be designed to include or permit the inclusionof information on the sealing sheet. For example the sealing sheet mayinclude a writeable area and/or a computer readable message or symbolsuch as a barcode.

[0241] Sealing sheets also may be designed to control the amount oflight that may pass through the sheet. A sheet may be substantiallyoptically transparent to permit light to pass, for example, so that anoptical analysis can be performed through the sheet. Alternatively, asheet may be substantially optically opaque to prevent light frompassing, for example, to reduce photobleaching. A suitable transparentsealing sheet may be made of a clear plastic, and a suitable opaquesealing sheet may be made of aluminum or an aluminized material.

[0242]FIG. 41 also shows a microplate 4120 and a sealing sheet 4122covering sample wells 4124 in the microplate. Recesses 4128 are formedin a perimeter portion of microplate 4120 to expose edge regions ofsealing sheet 4122 to facilitate removal of the sealing sheet by anautomated or robotic device 4130. Robotic device 4130 may include agripping mechanism and/or picking member for gripping and/or engagingexposed edges of sealing sheet 4122. The robotic device may use a numberof different mechanisms to lift sheet 4122 off microplate 4120. Forexample, the robotic device may grab or clamp the edge of sheet 4122 andthen lift the sheet off the microplate. Toward this end, recesses 4128generally comprise any open area (such as notches) adjacent sealingsheet 4122 sufficient to permit grasping and subsequent pulling of thesheet. The robotic device also may pierce and then lift sheet 4122, orapply a vacuum to and then lift sheet 4122. The robotic device also mayapply an adhesive to at least a portion of sheet 4122 before lifting thesheet off microplate 4120.

[0243]FIG. 42 is a partial view of an automated sealing-sheetapplication system. A conveyor 4150 carries a microplate 4152 in thedirection of arrow 4154 toward a sealing-sheet application site 4156. Atapplication site 4156, a sealing sheet 4158, shown in dashed lines onthe underside of a continuous carrier 4159, is applied precisely overthe sample containment region of microplate 4152. Successive discretesealing sheets are carried around a first roller 4160 in the directionof arrow 4162. Continuous carrier 4159 is rolled onto a second roller4163 after removal of sealing sheets at site 4156. The materials ofmicroplate 4152, sealing sheet 4158, and/or carrier 4159 may be selectedso that sheet 4158 can be reliably pressed onto microplate 4152 andreleased from carrier 4159. After applying sealing sheet 4158, conveyor4150 transports sealed microplate 4166 downstream.

[0244]FIG. 43 is a partial view of an automated sealing-sheet removalsystem. A conveyor 4170 transports a sealed microplate 4166 in thedirection of arrow 4172 toward a sealing-sheet removal site 4174. Atremoval site 4174, sheet 4158 is removed from microplate 4152 andtransferred to a continuous carrier 4176, which moves around roller 4178in the direction of arrow 4180. Uncovered microplate 4152 then movesdownstream on conveyor 4170. Transfer of sheets from microplate 4152 tocarrier 4176 at removal site 4174 may be achieved by selecting a carriermaterial, optionally containing an adhesive, that can bond to sheet 4158sufficiently to lift the sheet off microplate 4152.

[0245] Various mechanical mechanisms may be used to facilitate transferof a sealing sheet onto and off a microplate. For example, a pressuremember (e.g., mechanical press) may be applied from above the site. Italso may be helpful to provide Z-height adjustability of carriers 4159and 4176 above conveyors 4150 and 4170. It also may be helpful toprovide a mechanism for holding the microplate and/or the conveyor whenthe sealing sheet is being applied and/or removed.

[0246] Various mechanical mechanisms also may be used as a conveyor tomove microplates into and out of sealing-sheet application and removalstations. Such mechanisms include those described above (especially forthe intersite driver) under “Transport Module.”

[0247] The sealing-sheet application system and sealing-sheet removalsystem may be configured to enhance flexibility. For example, thesystems may be used alone as stand-alone units or together with oneanother and/or with other function modules as part of an integratedsystem. The systems also may be used with a variety of sample holders,including but not limited to microplates and other sample holdersdescribed above under “Sample Holders.”

[0248] The invention may provide a microplate sealing system that doesnot interfere with the stacking of covered microplates and/or leave anadhesive residue on a perimeter portion of the microplate after thesealing sheet is removed. Adhesive residue remaining on a top side of amicroplate after a sealing sheet is removed may cause stacked plates tostick together, causing a microplate-handling malfunction downstream.These problems may be substantially avoided by carefully controlling thedimension and placement of a sealing sheet on the top surface of amicroplate. Here, the sealing-sheet dimension may be matched to amicroplate so that the sheet substantially covers all of the wells inthe sample containment region of the microplate, while leaving a topperimeter portion of the microplate exposed for contacting anothermicroplate in a stack without interference. For use with standardmicroplates, the sealing sheets may be substantially rectangular, with awidth in the range of 2.75-inches to 3.25-inches, and a length in therange 4.25-inches to 4.75-inches.

[0249] 3. Sample Incubation Module

[0250]FIG. 44 shows an incubation module 4300 constructed in accordancewith aspects of the invention. The incubation module generally comprisesany mechanism or system for storing or incubating samples with controlof ambient environmental conditions, such as temperature, atmosphere(e.g., humidity, CO₂ level, etc.), agitation, and so on. The mechanismsmay include storing the samples in an environmentally controlledenclosure and/or using spacers or other mechanisms to increase thermaland gas exchange around and between samples. An incubation module may beused to protect thermally sensitive samples such as cells.

[0251] Environmental control is especially important with sample holderssuch as microplates that may be stacked atop one another before, during,and/or after analysis for transport, incubation, and/or storage.Microplates may be stacked to enhance convenience and minimizefootprint. For example, incubation module 4300 may support a stack ofmicroplates 4302 in the same shelf area used to support a singlemicroplate. Unfortunately, stacking microplates may limit thermal andgas exchange through the space between the microplates and therebycreate gradients in temperature and/or gas composition around thesamples. For example, samples contained in a microplate near the top ofa stack may be exposed to a substantially different temperature or gascomposition than samples contained in microplates near the bottom of thestack.

[0252] To facilitate environmental control, the incubation module 4300may include an enclosure 4304 for storing samples that may be partiallyor totally sealed from the outside environment. Moreover, the incubationmodule may include mechanisms for actively controlling the interiorenvironment within the enclosure. For example, incubation module 4300includes a valve device 4306 on a side of the enclosure for controllinggas flow into and out of the enclosure. Suitable gases such as CO₂ maybe injected into the enclosure from a gas source 4308 connected to thevalve and passively or actively removed from the enclosure to facilitatecirculation using a vent 4310, fan 4312, and/or other mechanism.Incubation module 4300 also includes heating and cooling elements 4314in or around the enclosure for raising or lowering the temperatureinside the enclosure. Heating and cooling may be effected from asuitable thermal source 4316. Incubation module 4300 also may includeagitation elements such as a rocker for rocking, shaking, and/orotherwise agitating enclosed sample holders to mix or aerate associatedsamples.

[0253] The incubation module may be used in conjunction with otherdevices and methods for increasing ambient heat and gas exchange aroundand between samples, especially samples in stacks of sample holders. Forexample, apertures might be provided in the side of a microplate toallow gas to circulate in the space between adjacently stackedmicroplates. Alternatively, or in addition, a spacing mechanism might beprovided atop or between microplates to separate a microplate fromadjacently stacked microplates.

[0254]FIG. 45 shows a microplate 4350 with adaptations for facilitatingenvironmental access between stacked microplates, with or without anintervening spacer. Microplate 4350 includes a frame portion 4352 and atop portion 4354 having a plurality of sample wells 4356. The frameportion includes apertures 4358 to allow thermal and gas circulationbetween plates. The top portion includes projections 4360 that extendabove a plane defined by the tops of the sample wells to support andelevate a microplate stacked above it, also to allow thermal and gascirculation between plates.

[0255]FIG. 46 shows portions of two alternative embodiments of alid-spacer 4400 for facilitating environmental access between stackedmicroplates. The lid-spacer may be stacked atop, between, or beneathmicroplates. The lid-spacer may include a lid portion 4402 and a spacerportion 4404.

[0256] Lid portion 4402 provides shape and structural support for thelid-spacer and regulates thermal and/or gas exchange over wells in amicroplate over which the lid-spacer is stacked. The lid portion mayinclude an exterior frame 4406 and a substantially planar cover portion4408 surrounded by the frame portion. The lid portion may fit sealinglyatop a microplate to seal a space over wells in the microplate, reducingevaporation. Alternatively, the lid portion may fit loosely atop amicroplate and/or include apertures 4410 in the frame or operates 4412in the cover portion to permit thermal and/or gas exchange over wells inthe microplate. Alternatively, or in addition, structures such as ridgesmay be provided on the bottom surface of the lid portion to allow gasdiffusion.

[0257] Spacer portion 4404 supports and elevates a microplate underwhich the lid-spacer is stacked, facilitating thermal and/or gasexchange under wells in the microplate. The spacer portion may includeprojections 4414 that extend upward from the lid portion to support amicroplate in a desired spaced orientation. These projections typicallywill be located at corners of the lid-spacer to enhance stability, butalso may be located along sides (especially long sides) of thelid-spacer.

[0258] The lid-spacer may be formed of any suitable material andmanufactured using any suitable method. A preferred material is plastic,such as that used to form microplates. Preferred manufacturing methodsinclude molding and/or standard machining operations.

[0259] The lid-spacer may be sized and shaped to mimic a typicalmicroplate, so that the lid-spacer can be handled (e.g., singulated) byequipment designed to handle a standard microplate. In this way, thelid-spacer may be singulated or re-stacked by a transport mechanism, andthe transport mechanism can perform de-lidding and re-liddingoperations, if programmed to do so. A possible sequence includes thefollowing steps: (1) singulate microplate from input stack, send tofunction module; (2) singulate lid-spacer from input stack, send tooutput stack; (3) send microplate from function module to output stack.This sequence can be repeated as desired.

[0260] A lid-spacer may be removed and replaced multiple times duringassay preparation, incubation, and/or detection. The lid-spacer mayinclude a bar code 4416 or reference fiducial and/or be sized or formedof a material permitting sample-handling equipment to distinguish itfrom a microplate or other sample holder. The lid-spacer may betransparent to permit light to pass for photoactivations or to perform aluminescence application through the lid-spacer. Alternatively, thelid-spacer may be opaque to preserve darkness inside the wells toprevent photobleaching prior to a luminescence application. Lid-spacerscan be placed at the top and bottom of a stack to ensure that plates arealways covered as plates are circulated back and forth in stacks duringassay preparation, incubation, and/or detection. A stack of microplateswith respective lid-spacers may be transported in a magazine back andforth between an incubator, detector, fluid dispenser, and/ortransporter when long-term incubations in a controlled environment arerequired.

[0261]FIG. 47 shows a stack 4450 of microplates 4452 and interveningspacing devices 4454. Spacing device 4454 is substantially the same asthe lid-spacer shown in FIG. 46. A singulation latch 4456 operates onthe bottom of the stack to remove one microplate or one spacing deviceat a time.

[0262] The incubation module may be used alone as a stand-alone unit ortogether with one or more other function modules as part of anintegrated system. FIG. 48 shows such an integrated system 4500, whichmay be used to process and analyze a sample contained in a microplate.System 4500 includes a microplate input site 4502, a fluidics module4504, an incubation module 4506, and an analysis module 4508. Atransport module 4510 transports microplates from site to site. Amicroplate 4512 is singulated from the bottom of a stack in input site4502. Transport module 4510 transports the microplate to fluidics module4504, where fluid is added to wells in the microplate. The microplate4512 is then transported and stacked in incubation module 4506, alongwith other microplates and intervening spacers and lids in accordancewith previously described embodiments of the invention. After thesamples are incubated in incubation module 4506, the microplate may besingulated from the bottom of a stack in the incubation module andtransported to analysis module 4508 where a test is performed on thesample.

[0263] The lid-spacer may be combined advantageously with a microplatesealer. It also may be advantageous to employ semipermeable films ormembranes selectively to control environmental access to samplescontained in wells under a spacer.

E. Analysis Module

[0264] The transport module, fluidics module, and/or auxiliary modulesdescribed in the preceding sections may be combined with an analysismodule to form an integrated system for sample preparation and/oranalysis. An analysis module generally comprises any mechanism or systemfor analyzing a sample, including qualitative analysis (to determine thenature of the sample and/or its components) and/or quantitative analysis(to determine the amount, relative proportions, and/or activity of thesample and/or its components).

[0265]FIG. 49 shows a system 5050 for analyzing samples that includes atransport module 5052 and an exemplary analysis module 5054 capable ofdetecting and analyzing light. The transport module includes I/O sites5056, a transfer site 5058, and mechanisms (not visible) fortransporting sample holders between the I/O and transfer sites, asdescribed above. The analysis module includes a housing 5060, a moveablecontrol unit 5062, an optical system (not visible), and a transportmechanism 5064. The housing may be used to enclose the analysis module,protecting both the user and components of the module. The control unitmay be used to operate the module manually and/or robotically, asdescribed in U.S. Pat. No. 6,025,985, which is incorporated herein byreference. The optical system and transport mechanisms are described insubsequent sections.

[0266] The analysis and transport modules may be configured so thattransport mechanism 5064 from analysis module 5054 can interact attransfer site 5058 with an intrasite driver (not visible) from transportmodule 5052 for sample transfer. More specifically, the transportmechanism may interact with an intrasite driver from the transportmodule, such as intrasite driver 2300 and lifters 2308 b in FIG. 23.

[0267] Further aspects of the analysis module are presented in thefollowing sections: (1) optical system, (2) transport mechanism, and (3)analytical methods.

[0268] 1. Optical System

[0269] FIGS. 50-53 show an optical system (and related components) 5090for use in system 5050. The optical system may include components forgenerating and/or detecting light, and for transmitting light to and/orfrom a sample. These components may include (1) a stage for supportingthe sample, (2) one or more light sources for delivering light to thesample, (3) one or more detectors for receiving light transmitted fromthe sample and converting it to a signal, (4) first and second opticalrelay structures for relaying light between the light source, sample,and detector, and/or (5) a processor for analyzing the signal from thedetector. Module components may be chosen to optimize speed,sensitivity, and/or dynamic range for one or more assays. For example,optical components with low intrinsic luminescence may be used toenhance sensitivity in luminescence assays by reducing background.Module components also may be shared by different assays, or dedicatedto particular assays. For example, steady-state photoluminescence assaysmay use a continuous light source, time-resolved photoluminescenceassays may use a time-varying light source, and chemiluminescence assaysmay not use a light source. Similarly, steady-state and time-resolvedphotoluminescence assays may both use a first detector, andchemiluminescence assays may use a second detector.

[0270] Optical system 5090 includes (a) a photoluminescence opticalsystem, and (b) a chemiluminescence optical system, as described below.Further aspects of the optical system are described in the followingpatent applications, which are incorporated herein by reference: U.S.patent application Ser. No. 09/160,533, filed Sep. 24, 1998; U.S. patentapplication Ser. No. 09/349,733, filed Jul. 8, 1999; PCT PatentApplication Ser. No. PCT/US99/16287, filed Jul. 26, 1999; and PCT PatentApplication Serial No. PCT/US00/04543, filed Feb. 22, 2000.

[0271] a. Photoluminescence Optical System

[0272] FIGS. 50-52 show the photoluminescence (or incident light-based)optical system of optical system 5090. As configured here, opticalsystem 5090 includes a continuous light source 5100 and a time-modulatedlight source 5102. Optical system 5090 includes light source slots 5103a-d for four light sources, although other numbers of light source slotsand light sources also could be provided. Light source slots 5103 a-dfunction as housings that may surround at least a portion of each lightsource, providing some protection from radiation and explosion. Thedirection of light transmission through the incident light-based opticalsystem is indicated by arrows.

[0273] Continuous source 5100 provides light for absorbance, scattering,photoluminescence intensity, and steady-state photoluminescencepolarization assays. Continuous light source 5100 may include arc lamps,incandescent lamps, fluorescent lamps, electroluminescent devices,lasers, laser diodes, and light-emifting diodes (LEDs), among others. Apreferred continuous source is a high-intensity, high color temperaturexenon arc lamp, such as a Model LX175F CERMAX xenon lamp from ILCTechnology, Inc. Color temperature is the absolute temperature in Kelvinat which a blackbody radiator must be operated to have a chromaticityequal to that of the light source. A high color temperature lampproduces more light than a low color temperature lamp, and it may have amaximum output shifted toward or into visible wavelengths andultraviolet wavelengths where many luminophores absorb. The preferredcontinuous source has a color temperature of 5600 Kelvin, greatlyexceeding the color temperature of about 3000 Kelvin for a tungstenfilament source. The preferred source provides more light per unit timethan flash sources, averaged over the flash source duty cycle,increasing sensitivity and reducing read times. Optical system 5090 mayinclude a modulator mechanism configured to vary the intensity of lightincident on the sample without varying the intensity of light producedby the light source. Further aspects of the continuous light source aredescribed in U.S. patent application Ser. No. 09/349,733, filed Jul. 8,1999, which is incorporated herein by reference.

[0274] Time-modulated source 5102 provides light for time-resolvedabsorbance and/or photoluminescence assays, such as photoluminescencelifetime and time-resolved photoluminescence polarization assays. Apreferred time-modulated source is a xenon flash lamp, such as a ModelFX-1160 xenon flash lamp from EG&G Electro-Optics. The preferred sourceproduces a “flash” of light for a brief interval before signal detectionand is especially well suited for time-domain measurements. Othertime-modulated sources include pulsed lasers, electronically modulatedlasers and LEDs, and continuous lamps and other sources whose intensitycan be modulated extrinsically using a Pockels cell, Kerr cell, or othermechanism. Such other mechanisms may include an amplitude modulator suchas a chopper as described in PCT Patent Application Ser. No.PCT/US99/16287, filed Jul. 26, 1999, which is incorporated herein byreference. Extrinsically modulated continuous light sources areespecially well suited for frequency-domain measurements.

[0275] In optical system 5090, continuous source 5100 and time-modulatedsource 5102 produce multichromatic, unpolarized, and incoherent light.Continuous source 5100 produces substantially continuous illumination,whereas time-modulated source 5102 produces time-modulated illumination.Light from these light sources may be delivered to the sample withoutmodification, or it may be filtered to alter its intensity, spectrum,polarization, or other properties.

[0276] Light produced by the light sources follows an excitation opticalpath to an examination site or measurement region. Such light may passthrough one or more “spectral filters,” which generally comprise anymechanism for altering the spectrum of light that is delivered to thesample. Spectrum refers to the wavelength composition of light. Aspectral filter may be used to convert white or multichromatic light,which includes light of many colors, into red, blue, green, or othersubstantially monochromatic light, which includes light of one or only afew colors. In optical system 5090, spectrum is altered by an excitationinterference filter 5104, which preferentially transmits light ofpreselected wavelengths and preferentially absorbs light of otherwavelengths. For convenience, excitation interference filters 5104 maybe housed in an excitation filter wheel 5106, which allows the spectrumof excitation light to be changed by rotating a preselected filter intothe optical path. Spectral filters also may separate light spatially bywavelength. Examples include gratings, monochromators, and prisms.

[0277] Spectral filters are not required for monochromatic (“singlecolor”) light sources, such as certain lasers, which output light ofonly a single wavelength. Therefore, excitation filter wheel 5106 may bemounted in the optical path of some light source slots 5103 a,b, but notother light source slots 5103 c,d. Alternatively, the filter wheel mayinclude a blank station that does not affect light passage.

[0278] Light next passes through an excitation optical shuttle (orswitch) 5108, which positions an excitation fiber optic cable 5110 a,bin front of the appropriate light source to deliver light to top orbottom optics heads 5112 a,b, respectively. Light is transmitted througha fiber optic cable much like water is transmitted through a gardenhose. Fiber optic cables can be used easily to turn light around comersand to route light around opaque components of the apparatus. Moreover,fiber optic cables give the light a more uniform intensity profile. Apreferred fiber optic cable is a fused silicon bundle, which has lowautoluminescence. Despite these advantages, light also can be deliveredto the optics heads using other mechanisms, such as mirrors.

[0279] Light arriving at the optics head may pass through one or moreexcitation “polarization filters,” which generally comprise anymechanism for altering the polarization of light. Excitationpolarization filters may be included with the top and/or bottom opticshead. In optical system 5090, polarization is altered by excitationpolarizers 5114, which are included only with top optics head 5112 a fortop reading; however, such polarizers also can be included with bottomoptics head 5112 b for bottom reading. Excitation polarization filters5114 may include an s-polarizer S that passes only s-polarized light, ap-polarizer P that passes only p-polarized light, and a blank O thatpasses substantially all light, where polarizations are measuredrelative to the beamsplitter. Excitation polarizers 5114 also mayinclude a standard or ferro-electric liquid crystal display (LCD)polarization switching system. Such a system may be faster than amechanical switcher. Excitation polarizers 5114 also may include acontinuous mode LCD polarization rotator with synchronous detection toincrease the signal-to-noise ratio in polarization assays. Excitationpolarizers 5114 may be incorporated as an inherent component in somelight sources, such as certain lasers, that intrinsically producepolarized light. Further aspects of the polarization filters and theiruse in polarization assay are described in U.S. patent application Ser.No. 09/349,733, filed Jul. 8, 1999, which is incorporated herein byreference.

[0280] Light at one or both optics heads also may pass through anexcitation “confocal optics element,” which generally comprises anymechanism for focusing light into a “sensed volume.” In optical system5090, the confocal optics element includes a set of lenses 5117 a-c andan excitation aperture 5116 placed in an image plane conjugate to thesensed volume, as shown in FIG. 52. Aperture 5116 may be implementeddirectly, as an aperture, or indirectly, as the end of a fiber opticcable. Preferred apertures have diameters of 1 mm and 1.5 mm. Lenses5117 a,b project an image of aperture 5116 onto the sample, so that onlya preselected or sensed volume of the sample is illuminated. The area ofillumination will have a diameter corresponding to the diameter of theexcitation aperture.

[0281] Light traveling through the optics head is directed onto abeamsplitter 5118, which reflects light toward a sample 5120 andtransmits light toward a light monitor 5122. The reflected light passesthrough lens 5117 b, which is operatively positioned betweenbeamsplitter 5118 and sample 5120.

[0282] Beamsplitter 5118 is used to direct excitation or incident lighttoward the sample and light monitor, and to direct light leaving thesample toward the detector. The beamsplitter is changeable, so that itmay be optimized for different assay modes or samples. In someembodiments, switching between beamsplitters may be performed manually,whereas in other embodiments, such switching may be performedautomatically. Automatic switching may be performed based on directoperator command, or based on an analysis of the sample by theinstrument. If a large number or variety of photoactive molecules are tobe studied, the beamsplitter must be able to accommodate light of manywavelengths; in this case, a “50:50” beamsplitter that reflects half andtransmits half of the incident light independent of wavelength isoptimal. Such a beamsplitter can be used with many types of molecules,while still delivering considerable excitation light onto the sample,and while still transmitting considerable light leaving the sample tothe detector. If one or a few related photoactive molecules are to bestudied, the beamsplitter needs only to be able to accommodate light ata limited number of wavelengths; in this case, a “dichroic” or“multidichroic” beamsplitter is optimal. Such a beamsplitter can bedesigned with cutoff wavelengths for the appropriate sets of moleculesand will reflect most or substantially all of the excitation andbackground light, while transmitting most or substantially all of theemission light in the case of luminescence. This is possible because thebeamsplitter may have a reflectivity and transmissivity that varies withwavelength.

[0283] The beamsplitter more generally comprises any optical device fordividing a beam of light into two or more separate beams. A simplebeamsplitter (such as a 50:50 beamsplitter) may include a very thinsheet of glass inserted in the beam at an angle, so that a portion ofthe beam is transmitted in a first direction and a portion of the beamis reflected in a different second direction. A more sophisticatedbeamsplitter (such as a dicbroic or multi-dichroic beamsplitter) mayinclude other prismatic materials, such as fused silica or quartz, andmay be coated with a metallic or dielectric layer having the desiredtransmission and reflection properties, including dichroic andmulti-dichroic transmission and reflection properties. In somebeamsplitters, two right-angle prisms are cemented together at theirhypotenuse faces, and a suitable coating is included on one of thecemented faces. Further aspects of the beamsplitter are described in PCTPatent Application Ser. No. PCT/US00/06841, filed Mar. 15, 2000, whichis incorporated herein by reference.

[0284] Light monitor 5122 is used to correct for fluctuations in theintensity of light provided by the light sources. Such corrections maybe performed by reporting detected intensities as a ratio overcorresponding times of the luminescence intensity measured by thedetector to the excitation light intensity measured by the lightmonitor. The light monitor also can be programmed to alert the user ifthe light source fails. A preferred light monitor is a siliconphotodiode with a quartz window for low autoluminescence.

[0285] The sample (or composition) may be held in a sample holdersupported by a stage 5123. The sample can include compounds, mixtures,surfaces, solutions, emulsions, suspensions, cell cultures, fermentationcultures, cells, tissues, secretions, and/or derivatives and/or extractsthereof. Analysis of the sample may involve measuring the presence,concentration, or physical properties (including interactions) of aphotoactive analyte in such a sample. Sample may refer to the contentsof a single microplate well, or several microplate wells, depending onthe assay. In some embodiments, such as a portable apparatus, the stagemay be intrinsic to the instrument.

[0286] The sample holder can include microplates, biochips, or anyarrangement of samples in a known format, as described above. In opticalsystem 5090, the preferred sample holder is a microplate 5124, whichincludes a plurality of microplate wells 5126 for holding samples.Microplates are typically substantially rectangular holders that includea plurality of sample wells for holding a corresponding plurality ofsamples. These sample wells are normally cylindrical in shape althoughrectangular or other shaped wells are sometimes used. The sample wellsare typically disposed in regular arrays. The “standard” microplateincludes 96 cylindrical sample wells disposed in a 8×12 rectangulararray on 9 millimeter centers.

[0287] The sensed volume typically has an hourglass shape, with a coneangle of about 25° and a minimum diameter ranging between 0.1 mm and 2.0mm. For 96-well and 384-well microplates, a preferred minimum diameteris about 1.5 mm. For 1536-well microplates, a preferred minimum diameteris about 1.0 mm. The size and shape of the sample holder may be matchedto the size and shape of the sensed volume, as described in U.S. patentapplication Ser. No. 09/062,472, filed Apr. 17, 1998, which isincorporated herein by reference.

[0288] The position of the sensed volume can be moved precisely withinthe sample to optimize the signal-to-noise and signal-to-backgroundratios. For example, the sensed volume may be moved away from walls inthe sample holder to optimize signal-to-noise and signal-to-backgroundratios, reducing spurious signals that might arise from luminophoresbound to the walls and thereby immobilized. In optical system 5090,position in the X,Y-plane perpendicular to the optical path iscontrolled by moving the stage supporting the sample, whereas positionalong the Z-axis parallel to the optical path is controlled by movingthe optics heads using a Z-axis adjustment mechanism 5130, as shown inFIGS. 50 and 51. However, any mechanism for bringing the sensed volumeinto register or alignment with the appropriate portion of the samplealso may be employed. For example, the optics head also may be scannedin the X,Y-plane, as described in U.S. Provisional Patent ApplicationSer. No. 60/142,721, filed Jul. 7, 1999, which is incorporated herein byreference.

[0289] The combination of top and bottom optics permits assays tocombine: (1) top illumination and top detection, or (2) top illuminationand bottom detection, or (3) bottom illumination and top detection, or(4) bottom illumination and bottom detection. Same-side illumination anddetection, (1) and (4), is referred to as “epi” and is preferred forphotoluminescence and scattering assays. Opposite-side illumination anddetection, (2) and (3), is referred to as “trans” and has been used inthe past for absorbance assays. In optical system 5090, epi modes aresupported, so the excitation and emission light travel the same path inthe optics head, albeit in opposite or anti-parallel directions.However, trans modes also can be used with additional sensors, asdescribed below. In optical system 5090, top and bottom optics headsmove together and share a common focal plane. However, in otherembodiments, top and bottom optics heads may move independently, so thateach can focus independently on the same or different sample planes.

[0290] Generally, top optics can be used with any sample holder havingan open top, whereas bottom optics can be used only with sample holdershaving optically transparent bottoms, such as glass or thin plasticbottoms. Clear bottom sample holders are particularly suited formeasurements involving analytes that accumulate on the bottom of theholder.

[0291] Light may be transmitted by the sample in multiple directions. Aportion of the transmitted light will follow an emission pathway to adetector. Transmitted light passes through lens 5117 c and may passthrough an emission aperture 5131 and/or an emission polarizer 5132. Inoptical system 5090, the emission aperture is placed in an image planeconjugate to the sensed volume and transmits light substantiallyexclusively from this sensed volume. In optical system 5090, theemission apertures in the top and bottom optical systems are the samesize as the associated excitation apertures, although other sizes alsomay be used. The emission polarizers are included only with top opticshead 5112 a. The emission aperture and emission polarizer aresubstantially similar to their excitation counterparts. Emissionpolarizer 5132 may be included in detectors that intrinsically detectthe polarization of light.

[0292] Excitation polarizers 5114 and emission polarizers 5132 may beused together in nonpolarization assays to reject certain backgroundsignals. Luminescence from the sample holder and from luminescentmolecules adhered to the sample holder is expected to be polarized,because the rotational mobility of these molecules should be hindered.Such polarized background signals can be eliminated by “crossing” theexcitation and emission polarizers, that is, setting the angle betweentheir transmission axes at 90°. As described above, such polarizedbackground signals also can be reduced by moving the sensed volume awayfrom walls of the sample holder. To increase signal level, beamsplitter5118 should be optimized for reflection of one polarization andtransmission of the other polarization. This method will work best wherethe luminescent molecules of interest emit relatively unpolarized light,as will be true for small luminescent molecules in solution.

[0293] Transmitted light next passes through an emission fiber opticcable 5134 a,b to an emission optical shuttle (or switch) 5136. Thisshuttle positions the appropriate emission fiber optic cable in front ofthe appropriate detector. In optical system 5090, these components aresubstantially similar to their excitation counterparts, although othermechanisms also could be employed.

[0294] Light exiting the fiber optic cable next may pass through one ormore emission “intensity filters,” which generally comprise anymechanism for reducing the intensity of light. Intensity refers to theamount of light per unit area per unit time. In optical system 5090,intensity is altered by emission neutral density filters 5138, whichabsorb light substantially independent of its wavelength, dissipatingthe absorbed energy as heat. Emission neutral density filters 5138 mayinclude a high-density filter H that absorbs most incident light, amedium-density filter M that absorbs somewhat less incident light, and ablank O that absorbs substantially no incident light. These filters maybe changed manually, or they may be changed automatically, for example,by using a filter wheel. Intensity filters also may divert a portion ofthe light away from the sample without absorption. Examples include beamsplitters, which transmit some light along one path and reflect otherlight along another path, and diffractive beam splitters (e.g.,acousto-optic modulators), which deflect light along different pathsthrough diffraction. Examples also include hot mirrors or windows thattransmit light of some wavelengths and absorb light of otherwavelengths.

[0295] Light next may pass through an emission interference filter 5140,which may be housed in an emission filter wheel 5142. In optical system5090, these components are substantially similar to their excitationcounterparts, although other mechanisms also could be employed. Emissioninterference filters block stray excitation light, which may enter theemission path through various mechanisms, including reflection andscattering. If unblocked, such stray excitation light could be detectedand misidentified as photoluminescence, decreasing thesignal-to-background ratio. Emission interference filters can separatephotoluminescence from excitation light because photoluminescence haslonger wavelengths than the associated excitation light. Luminescencetypically has wavelengths between 200 and 2000 nanometers.

[0296] The relative positions of the spectral, intensity, polarization,and other filters presented in this description may be varied withoutdeparting from the spirit of the invention. For example, filters usedhere in only one optical path, such as intensity filters, also may beused in other optical paths. In addition, filters used here in only topor bottom optics, such as polarization filters, may also be used in theother of top or bottom optics or in both top and bottom optics. Theoptimal positions and combinations of filters for a particularexperiment will depend on the assay mode and the sample, among otherfactors.

[0297] Light last passes to a detector, which is used in absorbance,scattering and photoluminescence assays, among others. In optical system5090, there is one detector 5144, which detects light from all modes. Apreferred detector is a photomultiplier tube (PMT). Optical system 5090includes detector slots 5145 a-d for four detectors, although othernumbers of detector slots and detectors also could be provided.

[0298] More generally, detectors comprise any mechanism capable ofconverting energy from detected light into signals that may be processedby the apparatus, and by the processor in particular. Suitable detectorsinclude photomultiplier tubes, photodiodes, avalanche photodiodes,charge-coupled devices (CCDs), and intensified CCDs, among others.Depending on the detector, light source, and assay mode, such detectorsmay be used in a variety of detection modes. These detection modesinclude (1) discrete (e.g., photon-counting) modes, (2) analog (e.g.,current-integration) modes, and/or (3) imaging modes, among others, asdescribed in PCT Patent Application Ser. No. PCT/US99/03678.

[0299] b. Chemiluminescence Optical System

[0300]FIGS. 50, 51, and 53 show the chemiluminescence optical system ofoptical system 5090. Because chemiluminescence follows a chemical eventrather than the absorption of light, the chemiluminescence opticalsystem does not require a light source or other excitation opticalcomponents. Instead, the chemiluminescence optical system requires onlyselected emission optical components. In optical system 5090, a separatelensless chemiluminescence optical system is employed, which isoptimized for maximum sensitivity in the detection of chemiluminescence.

[0301] Generally, components of the chemiluminescence optical systemperform the same functions and are subject to the same caveats andalternatives as their counterparts in the incident light-based opticalsystem. The chemiluminescence optical system also can be used for otherassay modes that do not require illumination, such aselectrochemiluminescence.

[0302] The chemiluminescence optical path begins with a chemiluminescentsample 5120 held in a sample holder 5126. The sample and sample holderare analogous to those used in photoluminescence assays; however,analysis of the sample involves measuring the intensity of lightgenerated by a chemiluminescence reaction within the sample rather thanby light-induced photoluminescence. A familiar example ofchemiluminescence is the glow of the firefly.

[0303] Chemiluminescence light typically is transmitted from the samplein all directions, although most will be absorbed or reflected by thewalls of the sample holder. A portion of the light transmitted throughthe top of the well is collected using a chemiluminescence head 5150, asshown in FIG. 50, and will follow a chemiluminescence optical pathway toa detector. The direction of light transmission through thechemiluminescence optical system is indicated by arrows.

[0304] The chemiluminescence head includes a nonconfocal mechanism fortransmitting light from a sensed volume within the sample. Detectingfrom a sensed volume reduces contributions to the chemiluminescencesignal resulting from “cross talk,” which is pickup from neighboringwells. The nonconfocal mechanism includes a chemiluminescence baffle5152, which includes rugosities 5153 that absorb or reflect light fromother wells. The nonconfocal mechanism also includes a chemiluminescenceaperture 5154 that further confines detection to a sensed volume.

[0305] Light next passes through a chemiluminescence fiber optic cable5156, which may be replaced by any suitable mechanism for directinglight from the sample toward the detector. Fiber optic cable 5156 isanalogous to excitation and emission fiber optic cables 5110 a,b and5134 a,b in the photoluminescence optical system. Fiber optic cable 5156may include a transparent, open-ended lumen that may be filled withfluid. This lumen would allow the fiber optic to be used both totransmit luminescence from a microplate well and to dispense fluids intothe microplate well. The effect of such a lumen on the opticalproperties of the fiber optic could be minimized by employingtransparent fluids having optical indices matched to the optical indexof the fiber optic.

[0306] Light next passes through one or more chemiluminescence intensityfilters, which generally comprise any mechanism for reducing theintensity of light. In optical system 5090, intensity is altered bychemiluminescence neutral density filters 5158. Light also may passthrough other filters, if desired.

[0307] Light last passes to a detector, which converts light intosignals that may be processed by the apparatus. In optical system 5090,there is one chemiluminescence detector 5160. This detector may beselected to optimize detection of blue/green light, which is the typemost often produced in chemiluminescence. A preferred detection is aphotomultiplier tube, selected for high quantum efficiency and low darkcount at chemiluminescence wavelengths (400-500 nanometers).

[0308] 2. Transport Mechanism

[0309] FIGS. 54-57 show a transport mechanism or stage, which generallycomprises any mechanism for supporting a sample in a sample holder foranalysis by an analysis module. (The transport module also may be usedto support a sample for fluid dispensing, as described above.) Inanalysis module 5054, the stage includes a transporter 5600 and baseplatform 5700.

[0310] FIGS. 54-56 show transporter 5600, which includes a transporterbody 5602 and substantially parallel first and second transporterflanges 5604 a,b that extend outward from transporter body 5602. Firstand second transporter flanges 5604 a,b terminate in first and secondtransporter extensions 5606 a,b that turn in toward one another withoutcontacting one another. Transporter extensions 5606 a,b may be joined bya connector portion 5607. Transporter body 5602, flanges 5604 a,b, andextensions 5606 a,b lie substantially in a plane and define atransporter cavity 5608 that is larger than the expected peripheraldimension of any sample holders which the transporter is intended tosupport. The shape of this cavity is chosen to accommodate the shape ofthe preferred sample holders. In analysis module 5054, cavity 5608 isgenerally rectangular to accommodate generally rectangular sampleholders, such as microplates. In analysis module 5054, long sides of therectangular sample holder are positioned against flanges 5604 a,b.

[0311] Transporter 5600 includes a shelf structure and associated framestructure for supporting a microplate or other sample holder. Forexample, transporter shelves 5610 along portions of body 5602, flanges5604 a,b, and extensions 5606 a,b form a shelf structure that supportsthe bottom of the sample holder. The shelf structure also could includeother support mechanisms, such as pins or pegs.

[0312] The transporter also includes an automatic sample holderpositioning mechanism 5620 for positioning sample holders precisely andreproducibly within cavity 5608. Mechanism 5620 includes Y and X axispositioning arms 5622 a,b that contact the sample holder to control itsY and X position, respectively. Here, a Y axis is defined as generallyparallel to transporter flanges 5604 a,b, and an X axis is defined asperpendicular to the Y axis and generally parallel to transporterextensions 5606 a,b. Other coordinate systems also can be defined, solong as they include two noncolinear directions.

[0313] Y-axis positioning arm 5622 a lies substantially within a channel5624 in body 5602. Y-axis positioning arm 5622 a includes a rod 5626 a,which is bent at substantially right angles to form three substantiallycoplanar and equal-lengthed segments. A first end segment 5628 a of rod5626 a terminates near cavity 5608 in a bumper 5632 for engaging asample holder. A second end segment 5634 a of rod 5626 a terminates awayfrom cavity 5608 in an actuator tab 5636 a for controlling movement ofarm 5622 a. Actuator tab 5636 a is bent away from body 5602. First andsecond end segments 5628 a, 5634 a are substantially parallel. A middlesegment 5638 a of rod 5626 a connects the two end segments at theirnontabbed ends 5640, 5641. An X-axis biasing spring 5642 a having firstand second spring ends 5644, 5648 is slipped over rod 5626 a. Firstspring end 5644 is held to second end segment 5634 a of rod 5626 a by aclamping-type retaining ring 5650. Second spring end 5648 rests againsta rod bearing 5652. The Y-axis biasing spring extends substantiallyparallel to first and second end segments 5628 a, 5634 a. The force fromspring 5642 a is transmitted to rod 5626 a by the clamping action ofretaining ring 5650.

[0314] X-axis positioning arm 5622 b also lies substantially withinchannel 5624 in body 5602 and is similar to Y-axis positioning arm,except that (1) first end segment 5628 b is longer and middle segment5638 b is shorter in rod 5626 b of the X-axis positioning arm than inrod 5626 a of the Y-axis positioning arm, (2) first end segment 5628 aterminates in a lever tab 5653 in the X-axis positioning arm rather thanin bumper 5632 in the Y-axis positioning arm, and (3) the two rods bendin opposite directions between first end segments 5628 a,b and secondend segments 5634 a,b.

[0315] X-axis positioning arm 5622 b is connected via lever tab 5653 toan X-axis positioning lever 5654 that lies along transporter flange 5604b. X-axis positioning lever 5654 includes first and second leverprojections 5656, 5658 and is pivotally mounted about a lever pivot axis5659 to transporter 5600 near the intersection of body 5602 and flange5604 b. First lever projection 5656 is substantially perpendicular toflange 5604 b and abuts lever tab 5630 b on X-axis positioning arm 5622b for actuating the positioning lever. Second lever projection 5658 alsois substantially perpendicular to flange 5604 b and includes an edge5660 for contacting a sample holder.

[0316] Transporter 5600 functions as follows. For loading, thetransporter occupies a loading position substantially outside a housing.In this position, actuator tabs 5636 a,b abut an actuator bar 5670,shown in FIG. 57. In addition, biasing springs 5642 a,b are compressed,and bumper 5632 and second projection 5658 having edge 5660 are pulledout of cavity 5608. A person, robot, or mechanical stacker then canplace a sample holder into cavity 5608 so that the bottom of the sampleholder rests on shelves 5610. Cavity 5608 is larger than the sampleholder to facilitate this placement and to accommodate variations insample holder size.

[0317] In some configurations, connector portion 5607 may be removed,such that transporter 5600 has an open end. This open end permits amicroplate transfer device to enter cavity 5608 and the generallyrectangular area of the holder. The microplate transfer device may,after moving into the generally rectangular area, move down relative totransporter 5600, thereby gently placing the microplate into thegenerally rectangular area.

[0318] For reading, the transporter must deliver the sample holder to anexamination site inside the housing. In this process, the transportermoves parallel to second end segments 5634 a,b. and actuator tabs 5636a,b disengage actuator bar 5670. Biasing spring 5642 a pushes Y-axispositioning arm 5622 a toward cavity 5608. Bumper 5632 engages thesample holder and pushes it away from body 5602 until it abutsextensions 5606 a,b. Biasing spring 5642 b pushes X-axis positioning arm5622 b toward cavity 5608. Edge 5660 of second projection 5658 engagesthe sample holder and pushes it away from flange 5604 b until it abutsflange 5604 a.

[0319] As long as the sample holder is placed in any position on thelower guide shelves, it may be positioned (registered) precisely andreproducibly against a reference corner 5672 within cavity 5608 underthe action of both positioning arms. Biasing springs 5642 a,b can bechosen to have different strengths, so that the X-Y positioning actionis performed less or more forcefully. In analysis module 5054, middlesegment 5638 b and first lever projection 5656 of positioning lever 5654can be varied in length to cause registration to occur in series, firstalong the X-axis or first along the Y-axis, and second along the Y-axisor second along the X-axis, respectively. For example, reducing thelength of middle segment 5638 b and reducing the length of projection5656 will cause registration to occur first in the X-axis, and second inthe Y-axis.

[0320] Positioning lever 5654 and bumper 5632 are retracted when body5602 of the automatic microplate positioning transporter is moved to theeject position by the X,Y stage. Thus, the microplate is placed ontransporter shelf 5610 only when the lever and bumper are retracted. Twosprings 5642 a,b are attached to the rods, which run along the length ofthe transporter body and end perpendicular to the body. When thetransporter is moved to the eject position, the two perpendicular endsof the rods encounter a stop 5670, which consists of a rectangularstructure located above and parallel to the body. The stop prevents thetwo perpendicular ends of the actuators, and thus the actuators, frommoving with the transporter body. This causes the two springs tocontract, changing the position of the transporter arms and increasingthe amount of room for the microplate. The microplate then can be placedon the guide shelf of the body. When the body of the automaticmicroplate positioning transporter is moved back away from the stop, thetwo perpendicular ends of the actuators no longer are blocked, whichallows the actuators, springs, and transporter arms to move into theiroriginal position. The expansion of the springs pushes the microplateexactly into position, as defined by the reference comer.

[0321] Thus, components of transporter 5600 act as first and secondreleasable clamp mechanisms. The first releasable clamp mechanismapplies a force against a first (e.g., Y or X) side of the microplate,thereby securing the microplate in the holder. The second releasableclamp mechanism applies a force against a second (e.g., X or Y) side ofthe microplate, thereby securing the microplate in the holder from twosides. These clamp mechanisms may sandwich a microplate between thepositioning arms and opposing portions of the frame structure, such thatthe positioning arms function as pushers and the opposing portions ofthe frame structure function as bumpers for the clamp mechanisms.

[0322] The invention provides a method of automatically feedingmicroplates in and out of an analyzer. The method comprises (1)automatically delivering a microplate just outside an opening to theanalyzer, (2) moving a gripping device from inside the analyzer, throughthe opening, to a location immediately below the microplate; and (3)gently placing the microplate onto the gripping device. The methodfurther may comprise clamping the microplate in the holder by applying afirst force against a first side of the microplate, applying a secondforce against a second side of the microplate, and/or seriallyperforming the clamping steps.

[0323]FIG. 57 shows a base platform 5700 with drive mechanisms formoving a transporter 5702 between loading and examination positions orsites. As previously described, transporter 5702 includes flanges 5704a,b defining a cavity 5706 for receiving and gripping a microplate (notshown). A Y-axis drive mechanism 5707 is provided for moving transporter5702 along a first track 5708 relative to the Y-axis, from a loadingposition 5710 toward an examination position 5712. An X-axis drivemechanism 5713 is provided to move transporter 5702 to examinationposition 5712 along a second track 5714 relative to the X-axis.

[0324] In operation, a microplate is loaded in transporter 5702 atloading position 5710. This loading position may correspond to thetransfer site for a transport module, as shown in FIG. 49. Transporter5702 is then driven toward the examination site (and/or optional fluiddispense site 5716) by Y-axis drive mechanism 5707. A sensor (not shown)detects the presence of the sample holder. The analyzer may beconfigured automatically to read the microplate once the sensor detectsits presence, or the analyzer may be configured to signal the systemcontroller through a data port that a microplate has been received andthat the analyzer is ready to accept a command to begin reading. The X-and Y-axis drive mechanisms then operate together to align selectedmicroplate wells with an optical axis, substantially parallel to aZ-axis, along which a sensed volume for luminescence detection may bedefined by optical components contained in one or both of a top andbottom optics head positioned above and below base platform 5700,respectively.

[0325] Transporter 5700 thus may function both as a sample deliverydevice in and out of the analyzer, and as a moveable stage forsupporting the sample holder at the examination site (and/or at theoptional fluid dispense site). The cavity in the transporter permitsanalysis to be carried out from below the holder, when the transporteris functioning as a stage at the examination site.

[0326] X- and Y-axis drive mechanisms 5707 and 5713 may be controlled bya high-performance motion control system that maximizes throughput whileminimizing detection errors. A preferred high-performance control systemincludes precision five-phase stepper motors that employ encoderfeedback to move the microplate quickly and accurately to each readposition. The control system may optimize the acceleration/decelerationprofiles of the microplate to minimize shaking of fluid within themicroplate, for example, by minimizing “jerk” (the time rate of changeof the acceleration of the microplate). Alternatively, the controlsystem may increase throughput by moving plates more quickly, if highervariation in results due to increased shaking and settling time may betolerated.

[0327] 3. Analytical Methods

[0328] Analysis modules may be used to analyze a sample, qualitativelyor quantitatively, as described above. Suitable methods for suchanalysis may include spectroscopic, hydrodynamic, and imaging methods,among others, especially those adaptable to high-throughput analysis ofmultiple samples.

[0329] Spectroscopic methods may involve interaction of light (orwavelike particles) with matter, and may involve monitoring someproperty of the light that is changed due to the interaction. Suitablespectroscopic methods may include absorption, luminescence (includingphotoluminescence, chemiluminescence, and electrochemiluminescence),magnetic resonance (including nuclear and electron spin resonance),scattering (including light scattering, electron scattering, and neutronscattering), circular dichroism, and optical rotation, among others.Suitable photoluminescence methods may include fluorescence intensity(FLINT), fluorescence polarization (FP), fluorescence resonance energytransfer (FRET), fluorescence lifetime (FLT), total internal reflectionfluorescence (TIRF), fluorescence correlation spectroscopy (FCS), andfluorescence recovery after photobleaching (FRAP), as well as theirphosphorescence and higher-order-transition analogs, among others.

[0330] Hydrodynamic methods may involve interaction of a molecule orother compound with its neighbors, its solvent, and/or a matrix, and maybe used to characterize molecular size and/or shape, or to separate asample into its components. Suitable hydrodynamic methods may includechromatography, sedimentation, viscometry, and electrophoresis, amongothers.

[0331] Imaging methods may involve any method for visualizing a sampleor its components, including optical microscopy and electron microscopy,among others.

[0332] These and other methods such as luminescence lifetime-basedbackground subtraction are described in further detail in the patentapplications and publications listed above under “Cross-References,”which are incorporated herein by reference.

F. Additional Examples

[0333] This section describes selected additional aspects of theinvention, as recited in the following numbered paragraphs:

[0334] 1. A device for transferring fluid between first and secondlocations, the device comprising a mount, and at least one pin moveablyattached to the mount, each pin having a base portion and a tip portionextending away from the base portion, the base portion being configuredto be attached to the mount, and the tip portion being configured toretain a substantially reproducible volume of a fluid when brought intocontact with the fluid for transfer between the first and secondlocations.

[0335] 2. The device of paragraph 1, wherein the mount includes anelastomeric material.

[0336] 3. The device of paragraph 1, wherein the mount includes a framecapable of dynamically adjusting the arrangement of the pins.

[0337] 4. The device of paragraph 3, wherein the frame dynamicallyadjusts the vertical position of the pins relative to a sample.

[0338] 5. The device of paragraph 3, wherein the frame dynamicallyadjusts the horizontal position of the pins relative to a sample.

[0339] 6. The device of paragraph 1 further comprising a drive mechanismconfigured to move the mount between the first and second positions.

[0340] 7. The device of paragraph 1, the device configured to transferfluid to or from a sample container having a reference fiducial encodinginformation about the sample container, further comprising a readercapable of determining the information encoded in the referencefiducial.

[0341] 8. The device of paragraph 1, wherein the pin is configured totransfer an amount of fluid equal to one or fewer microliters.

[0342] 9. The device of paragraph 1, the device including at least threepins, wherein the pins are arranged in a regular array.

[0343] 10. The device of paragraph 9, wherein the array isone-dimensional.

[0344] 11. The device of paragraph 9, wherein the array istwo-dimensional.

[0345] 12. A device for dispensing fluid to a plurality of sample sitesin a sample holder, the device comprising (a) a dispense site configuredto support a sample holder having a plurality of sample wells, (b) adispense manifold having a plurality of dispense elements, each dispenseelement capable of dispensing fluid to a sample site, (c) a controllerconfigured to receive information regarding sample positions and toautomatically adjust the effective separation between the dispenseelements to correspond to the separation between the sample site in thesample holder, and (d) a registration device configured to bring thedispense elements and at least a portion of the sample site intoregister, so that fluid may be dispensed from the dispense elements tothe sample sites.

[0346] 13. The device of paragraph 12, wherein the dispense elements areconfigured for noncontact fluid dispensing.

[0347] 14. The device of paragraph 12, wherein the sample holder is amicroplate and the sample sites correspond to wells in the microplate.

[0348] 15. The device of paragraph 12, wherein the sample holder is asubstantially planar surface, and wherein the sample sites arepositioned in the substantially planar surface.

[0349] 16. The device of paragraph 12, the sample holder having a barcode encoding information regarding positions of sample sites, furthercomprising a bar code reader configured to scan the bar code.

[0350] 17. The device of paragraph 12, the sample holder having areference fiducial encoding information regarding positions of samplesites in the sample holder, further comprising a reference fiducialreader configured to read the reference fiducial.

[0351] 18. The device of paragraph 12 further including an imagingdevice configured to image at least a portion of the sample holder, sothat the positions of sample sites may be determined.

[0352] 19. The device of paragraph 12, the sample sites and dispenseelements being fixed, wherein the effective separation between thedispense elements may be adjusted to correspond to the separationbetween the sample sites in the sample holder by changing the relativeorientation of the dispense elements and sample sites.

[0353] 20. The device of paragraph 19, the dispense elements forming asubstantially linear array constrained to rotate about a pivot point,wherein the relative orientation of the sample sites and dispenseelements may be changed by rotating the dispense elements about thepivot point.

[0354] 21. The device of paragraph 12 further comprising dispensingfluid from the dispense elements to the sample sites.

[0355] 22. The device of paragraph 21, wherein the fluid is dispensedsimultaneously from each dispense element.

[0356] 23. The device of paragraph 21, wherein the fluid is dispensedsequentially from each dispense element.

[0357] 24. The device of paragraph 12, wherein the separations betweendispense elements are variable.

[0358] 25. The device of paragraph 12, wherein the separations betweendispense elements are fixed.

[0359] 26. The device of paragraph 12, wherein the dispense elements areconfigured to dispense a range of fluid volume including volumes of lessthan about 1 microliter.

[0360] 27. A method for dispensing fluid to a plurality of sample sitesin a sample holder, the method comprising (a) providing a fluiddispenser having a plurality of dispense elements, each dispense elementconfigured to dispense fluid, (b) providing a sample holder having aplurality of sample sites, each sample site configured to hold a fluid,(c) obtaining information regarding the positions of the sample sites inthe sample holder, (d) automatically adjusting the effective positionsof the dispense elements to correspond to the positions of the samplesites using the information regarding the positions of the sample sites,(e) bringing the dispense elements and at least a portion of the samplesites into register, and (f) dispensing fluid from the dispense elementsto the sample sites.

[0361] 28. The method of paragraph 27, wherein the step includes thestep of separating droplets from the dispense elements withoutcontacting the droplets to a surface.

[0362] 29. The method of paragraph 27, wherein the sample holder is amicroplate.

[0363] 30. The method of paragraph 27, wherein the sample holder has asubstantially planar surface, and wherein the sample sites arepositioned in the substantially planar surface.

[0364] 31. The method of paragraph 27, wherein the step of obtaininginformation includes scanning an area on the sample holder.

[0365] 32. The method of paragraph 31, wherein the pre-encodedinformation is encoded using a bar code, and wherein the sample isscanned using a bar code reader.

[0366] 33. The method of paragraph 27, wherein the step of obtaininginformation includes measuring the positions of the sample sites duringor immediately prior to dispensing fluid.

[0367] 34. The method of paragraph 33, wherein the step of measuring thepositions includes the step of imaging at least a portion of the sampleholder using an imaging device.

[0368] 35. The method of paragraph 33, wherein the step of measuring thepositions includes the steps of locating the position of a referencefiducial and inferring the positions of the sample sites from theposition of the reference fiducial by at least one of interpolation andextrapolation.

[0369] 36. The method of paragraph 27, the sample sites and dispenseelements being fixed, wherein the step of automatically adjusting theeffective positions of the dispense elements includes the step ofchanging the relative orientation of the sample sites and dispenseelements.

[0370] 37. The method of paragraph 36, the dispense elements forming asubstantially linear array constrained to rotate about a pivot point,wherein the step of changing the relative orientation of the samplesites and dispense elements includes the step of rotating the dispenseelements about the pivot point.

[0371] 38. The method of paragraph 27 further comprising dispensingfluid from the dispense elements to the sample sites.

[0372] 39. The method of paragraph 38, wherein the fluid is dispensedsimultaneously from each dispense element.

[0373] 40. The method of paragraph 38, wherein the fluid is dispensedsequentially from each dispense element.

[0374] 41. The method of paragraph 27 further comprising (a) providing asecond sample holder having a plurality of sample sites, each samplesite configured to hold a fluid, (b) obtaining information regarding thepositions of the sample sites in the second sample holder, and (c)automatically readjusting the effective positions of the dispenseelements to correspond to the positions of the sample sites in thesecond sample holder using the information regarding the positions ofthe sample sites in the second sample holder.

[0375] 42. The method of paragraph 41, wherein the separations betweendispense elements are variable.

[0376] 43. The method of paragraph 27, wherein the separations betweendispense elements are fixed.

[0377] 44. The method of paragraph 27, wherein the dispense elements arecapable of dispensing a fluid aliquot of less than about 1 microliter.

[0378] 45. A device for spacing microplates, the device comprising aspacing member dimensioned to maintain separation between stacked firstand second microplates.

[0379] 46. The device of paragraph 45, wherein the spacing memberincludes a lid portion.

[0380] 47. The device of paragraph 46, wherein the lid portionsubstantially covers the sample wells in a microplate stacked below.

[0381] 48. The device of paragraph 45, wherein the spacing member has aframe portion.

[0382] 49. The device of paragraph 48, wherein the frame portionsubstantially mimics a frame portion of a typical microplate so that astacker or destacker can manipulate the spacing member as it would amicroplate.

[0383] 50. The device of paragraph 48, wherein the frame portion has atleast one aperture for allowing environmental circulation betweenadjacently stacked microplates.

[0384] 51. The device of paragraph 45, wherein the spacing memberincludes one or more upwardly extending projections.

[0385] 52. The device of paragraph 46, wherein the lid portion has atleast one aperture for allowing environmental access to samplescontained in wells under the spacing member.

[0386] 53. A method of allowing environmental access between stackedmicroplates, the method comprising spacing adjacent microplates in astack.

[0387] 54. The method of paragraph 53 further comprising the step ofproviding at least one aperture in a side of a frame member betweenstacked microplates.

[0388] 55. The method of paragraph 53 further comprising the step ofcontrolling ambient gas constituents and temperature around and betweenstacked microplates.

[0389] 56. The method of paragraph 53 further comprising the step ofcirculating a gas between stacked microplates.

[0390] 57. A method of allowing environmental access between stackedmicroplates, the method comprising projecting spacing members betweenmicroplates in a stack.

[0391] 58. A method of allowing environmental access between stackedmicroplates, the method comprising elevating one microplate aboveanother microplate by situating a spacing member between themicroplates.

[0392] 59. The method of paragraph 58 further comprising the step ofconfiguring the spacing member to mimic the perimetral dimensions of atypical microplate so that the spacing member can be manipulated by amicroplate stacker or destacker.

[0393] 60. The method of paragraph 59 further comprising the step ofautomatically stacking and de-stacking the spacing member.

[0394] 61. A microplate comprising (a) a frame member, (b) a pluralityof sample wells contained within the frame member, the wells havingupper edges contained in a common plane, and (c) one or more projectionsextending above the plane, so that the wells maintain a spacedrelationship to a microplate stacked on top.

[0395] 62. A system for automatically covering and uncovering wells in amicroplate, the system comprising (a) a supply of flexible sheetmembers, (b) a sealing device that automatically positions a sealingsheet over an array of wells in a microplate, and presses the sealingsheet onto the microplate so that the wells are substantially sealed,and (c) a sheet removal device that automatically contacts and lifts thesealing sheet off the microplate.

[0396] 63. The system of paragraph 62, wherein the sheet removal devicehas a picking member that removes the sealing sheet by gripping an edgeof the sheet.

[0397] 64. The system of paragraph 62, wherein the sheet removal devicehas a picking member that pierces and then lifts the sheet from themicroplate.

[0398] 65. The system of paragraph 62, wherein the sheet removal devicehas a picking member that applies a vacuum to at least a portion of thesheet.

[0399] 66. The system of paragraph 62, wherein the sheet removal devicehas a picking member that applies an adhesive to at least a portion ofthe sealing sheet.

[0400] 67. A device for removing a sealing sheet from a microplate, thedevice comprising (a) a microplate-sheet removal station, and (b) asheet-handling mechanism positioned near the sheet removal station, andconfigured to contact and lift a sealing sheet off a sealed microplate.

[0401] 68. The device of paragraph 67, wherein the sheet-handlingmechanism has a picking member that grips an edge of the sheet.

[0402] 69. The device of paragraph 67, wherein the sheet-handlingmechanism has a picking member that pierces the sheet and then lifts thesheet from the microplate.

[0403] 70. The device of paragraph 67, wherein the sheet-handlingmechanism has a picking member that applies a vacuum to at least aportion of the sheet.

[0404] 71. The device of paragraph 67, wherein the sheet-handlingmechanism has a picking member that applies an adhesive to at least aportion of the sheet.

[0405] 72. A microplate sealing system comprising (a) a first microplatehaving a plurality of wells in a sample containment area, and a framearea surrounding the sample containment area, wherein the microplate isdesigned so that it can be stacked below a second microplate, and (b) aflexible sealing sheet covering the sample containment area of the firstmicroplate without contacting the second microplate when it is stackedon top of the first microplate.

[0406] 73. The system of paragraph 72, wherein the first microplate hasat least one recess in a side exposing top and bottom sides of an edgeof the sealing sheet for easy gripping and removal of the sheet from themicroplate.

[0407] 74. The system of paragraph 72, wherein the flexible sealingsheet is dimensioned to substantially cover the sample containment areaof the microplate without contacting the frame area of the microplate.

[0408] 75. The system of paragraph 72, wherein the flexible sealingsheet is substantially optically transparent relative to an opticalanalysis to be carried out on a sample contained in a well of themicroplate.

[0409] 76. The system of paragraph 72, wherein the flexible sealingsheet is substantially optically opaque.

[0410] 77. A cover material for microplates comprising (a) a continuousroll of backing material, and (b) a series of discrete sealing sheetsreleasably fixed on a surface of the backing material, wherein eachsheet is dimensioned to cover substantially all of a plurality of wellsof a standard microplate while leaving a peripheral top portion of themicroplate uncovered.

[0411] 78. A method of applying a cover sheet to a microplate, themethod comprising (a) applying a sealing sheet over substantially all ofthe wells in a microplate without covering a continuous perimetral topregion of the microplate, and (b) exposing top and bottom sides of anedge portion of the sealing sheet for gripping when the sealing sheet isremoved.

[0412] 79. The method of paragraph 78, wherein the applying step isperformed manually.

[0413] 80. The method of paragraph 78, wherein the applying step isautomated.

[0414] 81. The method of paragraph 78 further comprising the step ofremoving the sealing sheet from the microplate prior to performing ananalysis on a sample contained in a well in the microplate.

[0415] 82. The method of paragraph 81, wherein the removing step isperformed manually.

[0416] 83. The method of paragraph 81, wherein the removing step isautomated.

[0417] 84. The method of paragraph 78 further comprising the step offorming at least one recess in a side of the microplate so that top andbottom sides of the edge portion are exposed.

[0418] 85. The method of paragraph 78, wherein the sealing sheet issubstantially rectangular.

[0419] 86. A sample holder comprising (a) a top portion containing anarray of sample wells, and (b) a seal covering one or more of the wells,wherein top and bottom sides of an edge portion of the seal are exposedto facilitate removal of the seal.

[0420] 87. The sample holder of paragraph 86, wherein the top portionhas at least one recess below an edge of the seal.

[0421] 88. The sample holder of paragraph 86, wherein the top portionhas a plurality of recesses on at least two sides of the plate.

[0422] 89. The sample holder of paragraph 86, wherein the sample holderis a microplate.

[0423] 90. The sample holder of paragraph 86, wherein the seal issubstantially rectangular.

[0424] 91. A sample holder comprising a top portion containing an arrayof sample wells within a perimeter portion, wherein the top portion hasat least one recess in the perimeter portion for exposing an edge of aseal that covers one or more of the wells.

[0425] 92. An automated device comprising a gripping mechanismconfigured to contact an exposed edge of a sealing sheet on amicroplate, and to remove the sheet from the microplate.

[0426] 93. The automated device of paragraph 92, wherein the grippingmechanism pierces and lifts the sealing sheet from the microplate.

[0427] 94. The automated device of paragraph 92, wherein the grippingmechanism applies a vacuum to at least a portion of the sealing sheet.

[0428] 95. The automated device paragraph 92, wherein the grippingmechanism applies an adhesive to at least a portion of the sealingsheet.

[0429] 96. A first sample container device comprising (a) a baseportion, (b) a plurality of wells formed in a top side, the wells havingupper edges defining a plane above the base portion, and (c) at leastone elevation mechanism extending above the plane to hold a secondsample container in spaced relation to the first sample container.

[0430] 97. The device of paragraph 96, wherein the elevation mechanismincludes at least four post members connected to the top side andextending upward from the plane.

[0431] 98. The device of paragraph 96, wherein the elevation mechanismincludes four post members, each post member extending upward from acorner of the first sample container.

[0432] 99. The device of paragraph 96, wherein the elevation mechanismis independent from the first sample container.

[0433] 100. The device of paragraph 96, wherein the base portion has atleast one aperture to allow gas circulation under the wells.

[0434] 101. The device of paragraph 196, wherein wells are provided inthe top side of the first sample container in a density of at leastabout 4 wells per 81 mm².

[0435] 102. The device of paragraph 196, wherein the elevation mechanismhas a lid portion that substantially covers all of the wells in the topside of the first sample container.

[0436] 103. An incubation system, comprising (a) an enclosure, (b) atleast two microplates stacked within the enclosure, each microplatehaving a plurality of wells for containing samples, and (c) a spacingmechanism between the two plates to allow gas diffusion and thermalequilibration around samples contained in wells of the microplate.

[0437] 104. The system of paragraph 103, wherein the spacing mechanismhas an outer frame dimension similar to a microplate so that a stackingdevice designed to handle microplates can also handle the spacingmechanism.

[0438] 105. The system of paragraph 103, wherein at least one of themicroplates has a lateral aperture for allowing gas to circulate betweenthe plates.

[0439] 106. The system of paragraph 103, wherein the spacing mechanismis formed in a top side of one of the microplates.

[0440] 107. The system of paragraph 103, wherein the spacing mechanismis a separate piece from the two microplates.

[0441] 108. The system of paragraph 103, wherein the enclosure is aroom.

[0442] 109. The system of paragraph 103, wherein the enclosure is asealed chamber.

[0443] 110. The system of paragraph 103, wherein the enclosure has avalve for allowing controlled passage of gas in and out of theenclosure.

[0444] 111. A method of controlling a gas environment around a pluralityof samples, comprising (a) dispensing samples into a plurality of wellsin a first microplate and a second microplate, (b) stacking a spacingmechanism on top of the first microplate, and (c) stacking the secondmicroplate on top of the spacing mechanism to allow gas diffusion andthermal equilibration around the samples.

[0445] 112. The method of paragraph 111 further comprising the step ofproviding lateral apertures in the microplates.

[0446] 113. The method of paragraph 111 further comprising the step ofmonitoring the temperature of a space containing the microplates.

[0447] 114. The method of paragraph 111 further comprising the step ofincubating the microplates in an enclosure.

[0448] 115. A device for spacing microplates, the device comprising (a)first and second microplates, and (b) a spacing member separating thefirst and second microplates in a stack.

[0449] 116. The device of paragraph 115, wherein the spacing memberincludes a lid portion.

[0450] 117. The device of paragraph 115, wherein each microplate has aplurality of sample wells, the lid portion substantially covering thesample wells so that evaporation from the sample wells is minimizedwhile allowing thermal communication between the environment and thespace between the microplates.

[0451] 118. The device of paragraph 115, wherein the spacing member hasa frame portion, the frame portion being designed to substantially mimica frame portion of a typical microplate so that a stacker or destackercan manipulate the spacing member as it would a microplate.

[0452] 119. The device of paragraph 118, wherein the frame portion hasat least one aperture for allowing gas and thermal circulation betweenthe microplates.

[0453] 120. The device of paragraph 115, wherein the spacing memberincludes one or more upwardly extending projections.

[0454] 121. The device of paragraph 114, wherein the lid portion has atleast one aperture for allowing environmental access to samplescontained in wells under the spacing member.

[0455] Although the invention has been disclosed in preferred forms, thespecific embodiments thereof as disclosed and illustrated herein are notto be considered in a limiting sense, because numerous variations arepossible. Applicants regard the subject matter of their invention toinclude all novel and nonobvious combinations and subcombinations of thevarious elements, features, functions, and/or properties disclosedherein. No single feature, function, element or property of thedisclosed embodiments is essential. The following claims define certaincombinations and subcombinations of features, functions, elements,and/or properties that are regarded as novel and nonobvious. Othercombinations and subcombinations may be claimed through amendment of thepresent claims or presentation of new claims in this or a relatedapplication. Such claims, whether they are broader, narrower, or equalin scope to the original claims, also are regarded as included withinthe subject matter of applicant's invention.

We claim:
 1. A system for delivering fluid to a sample holder comprisinga fluid source, a pump connected to the fluid source, a dispenserassembly having an orifice, and a conduit path extending from the pumpto the orifice of the dispenser assembly, the conduit path remainingopen and unconstricted between successive non-contact deposition offluid aliquots having a volume of less than about 5 microliters peraliquot.
 2. The system of claim 1 further comprising a controller thatdetermines the volume of each fluid aliquot.
 3. The system of claim 1 ,wherein the pump device pumps incrementally at a rate corresponding tothe rate of aliquot deposition.
 4. The system of claim 1 , wherein thedispenser assembly has a hydrophobic tip portion.
 5. The system of claim4 , wherein the tip portion is made of a heat-shrinkable material. 6.The system of claim 5 , wherein the tip portion is made of materialselected from the group consisting of PTFE, polypropylene, polyethylene,and FEP.
 7. The system of claim 1 , wherein the dispenser assembly has atip portion made of sapphire.
 8. The system of claim 1 , wherein theorifice is formed at an end of a tube-like tip portion, the tip portionhaving a wall thickness around the orifice of less than about 8thousandths of an inch.
 9. The system of claim 1 , wherein the orificehas an inner diameter of less than about 200-microns.
 10. The system ofclaim 1 , wherein the pump is connected to the dispenser assembly by atube having a distal end, the tip portion having a flange on a proximalend, the distal end of the tube being held in contact with the flange ofthe tip portion.
 11. The system of claim 1 , wherein the pump is asyringe pump.
 12. The system of claim 11 , wherein the syringe pump hasa linear motor.
 13. The system of claim 11 , wherein the pump has astepper motor.
 14. The system of claim 10 , wherein the dispenserassembly includes a manifold for holding the distal end of the tube incontact with the flange of the tip portion.
 15. The system of claim 14 ,wherein the same manifold secures connection of a plurality of tubes torespective tip portions to define an array of fluid dispensing channels.16. The system of claim 15 , wherein the array of fluid dispensingchannels corresponds to an array of wells in a microplate.
 17. Thesystem of claim 15 , wherein the array of fluid dispensing channelscorresponds to an array of sites on a biochip.
 18. The system of claim15 , wherein the array corresponds to wells in a standard 96-wellmicroplate.
 19. The system of claim 15 further comprising a sampleholder registration mechanism that alters the position of a sampleholder relative to the manifold so that the same array of fluiddispensing channels can be used to deposit fluid into sample holdershaving varying densities of deposition sites.
 20. A fluid dispensingassembly comprising a manifold device having a plurality of apertures, aplurality of tip devices, each tip device having a conduit channelconnected contiguously with an aperture in the manifold, each tip devicebeing made of a heat-shrinkable hydrophobic material and having a wallthickness small enough so that droplets of less than 5 microliters perdroplet can be separated from the tip device without contacting thedroplets to a surface and without closing or constricting the conduitchannel.
 21. The assembly of claim 20 further comprising a plurality ofpumps, each pump being connected to a tip device.
 22. The assembly ofclaim 21 , wherein the pumps are syringe pumps.
 23. The assembly ofclaim 21 , wherein each pump has a stepper motor.
 24. The assembly ofclaim 21 , wherein each pump has a linear motor.
 25. The assembly ofclaim 20 further comprising a fluid source station having one or morereservoirs, the pumps being connected to said one or more reservoirs.26. The assembly of claim 25 further comprising an interchangeableconduit network allowing any combination of tip devices to be connectedto any one of the reservoirs.
 27. The assembly of claim 20 , whereineach tip device has a circumferential wall defining an orifice, the wallhaving a thickness that is less than about 8 thousandths of an inch. 28.The system of claim 20 , wherein each tip device is made of ahydrophobic material.
 29. The system of claim 28 , wherein each tipdevice is made of a material selected from the group consisting of PTFE,polypropylene, polyethylene, and FEP.
 30. A fluid dispensing systemcomprising an array of N dispense tips, each dispense tip beingconnected to a separate syringe pump, a fluid source bank, the fluidsource bank having X number of fluid reservoirs, where X is in the rangeof 1 to N, and a changeable fluid conduit network capable of permitting:(a) each pump to be connected to a separate fluid reservoir, (b) eachpump to be connected to the same fluid reservoir, (c) any subset ofpumps to be connected to the same fluid reservoir while one or moreother tips are connected to another fluid reservoir.
 31. The system ofclaim 30 , wherein the dispense tips are configured to dispense dropletsin a range of volumes including volumes of less than about 5 microlitersper droplet without contacting the droplet to a surface.
 32. The systemof claim 31 , wherein each dispense tip has a hydrophobic wall definingan orifice having a diameter of less than about 200 microns, the wallhaving a thickness of less than about 8 thousandths of an inch.
 33. Thesystem of claim 30 , wherein the dispense tips are made of a materialselected from the group consisting of sapphire, PTFE, polypropylene,polyethylene, and FEP.
 34. The system of claim 30 , wherein each pumpincludes a linear motor.
 35. A device for dispensing fluid to a sampleor sample holder, the device comprising a fluid reservoir, a pump deviceconnected to the fluid reservoir, and a dispense element operativelyconnected to the pump device, wherein the pump device drives fluidincrementally to the dispense element with sufficient velocity andacceleration so that a fluid aliquot of less than about five microlitersseparates from the dispense element without contacting a surface. 36.The device of claim 35 , wherein the dispense element has a hydrophobictip with a tube-like wall defining an orifice and is configured toreduce the affinity of dispensed fluid for the dispense element, so thatdispensed fluid separates from the dispense element.
 37. The device ofclaim 36 , wherein the wall of the tip has a thickness of less thanabout 8 thousandths of an inch.
 38. The device of claim 36 , wherein theorifice has a diameter of less than about 200 microliters.
 39. Thedevice of claim 35 , wherein the dispense element has a tip portion madeof a material selected from the group consisting of PTFE, polypropylene,polyethylene, and FEP.
 40. A method of dispensing fluid aliquots of lessthan about 1 microliter per aliquot comprising connecting a pump to adispense tip via a conduit path, pulsing fluid through the conduit path,and ejecting a fluid aliquot of less than about 1 microliter from thedispense tip for each fluid pulse.
 41. The method of claim 40 , whereinthe ejecting step is carried out without closing or constricting theconduit path.
 42. The method of claim 40 further comprising the step ofdirecting ejected fluid aliquots into wells of a microplate.
 43. Themethod of claim 40 further comprising the step of directing ejectedfluid aliquots to sites on a biochip.
 44. The method of claim 40 furthercomprising the step of minimizing interfacial attraction between thedispense tip and the fluid by using a hydrophobic dispense tip, thedispense tip having a wall defining an orifice, the wall having athickness of less than about eight thousandths of an inch.
 45. A fluiddispensing system comprising a fixed two dimensional array of dispensetips that are capable of non-contact deposition of fluid aliquots ofless than about 5 microliters per aliquot simultaneously into aplurality of rows of wells in a microplate.
 46. A fluid dispensingsystem comprising a syringe pump having a linear motor, and a dispensetip connected to the pump for depositing a fluid aliquot to a sampleholder.
 47. The system of claim 46 , wherein the syringe pump has alinear stepper motor.
 48. The system of claim 46 , wherein the syringepump has a linear servo motor.
 49. An integrated high throughputanalysis system comprising an assay preparation unit that combinesreagents and samples in wells of a microplate, an analyzer integratedwith the assay preparation unit, wherein the analyzer includes opticsthat are substantially matched to the wells of the microplate, and acontroller that can be programmed to oversee assay preparation andanalysis.
 50. The system of claim 49 , wherein the assay preparationunit includes a fluid dispensing system.
 51. The system of claim 49 ,wherein the fluid dispensing system includes an array of dispense tipsthat are capable of non-contact dispensing of droplets of less thanabout 5 microliters per droplet.
 52. The system of claim 51 furthercomprising a registration device capable of moving the array of dispensetips relative to the microplate so that the same array of dispense tipscan be used to dispense fluid into microplates having differentdensities of wells.
 53. The system of claim 49 , wherein the assaypreparation unit includes two microplate stacking stations, each of thestacking stations including a singulation mechanism that is capable ofadding and subtracting a microplate to and from the bottom a microplatestack.
 54. The system of claim 49 , wherein the analyzer is programmedto receive information based on detection of a reference fiducial in themicroplate.
 55. The system of claim 49 , wherein each well in themicroplate has a frusto-conical shape.
 56. The system of claim 49 ,wherein the assay preparation unit includes an incubation chamber. 57.The system of claim 56 further comprising lid-spacing devices thatseparate adjacent microplates in the incubation chamber.
 58. The systemof claim 50 , wherein the assay preparation system includes a cyclingmechanism that allows a microplate to be cycled automatically throughthe fluid dispensing station multiple times.